final planned file move

author: Eric Messick <ericm@nanorex.com> 2008-03-14 04:44:50 +0000
committer: Eric Messick <ericm@nanorex.com> 2008-03-14 04:44:50 +0000
commit: bcacffeade3f8571f4ba9f7545e0e1afeab8b072 (patch)
tree: 6c93c2690a3649102452967e1b3939704a2404fb
parent: 1ff69ade95165adbeb0eae702be3731a7b5e70bb (diff)
download: nanoengineer-theirix-bcacffeade3f8571f4ba9f7545e0e1afeab8b072.tar.gz
nanoengineer-theirix-bcacffeade3f8571f4ba9f7545e0e1afeab8b072.zip
365 files changed, 1412 insertions, 1415 deletions
diff --git a/cad/src/Makefile b/cad/src/Makefile
index 38725b742..23a920d03 100755
--- a/cad/src/Makefile
+++ b/cad/src/Makefile
@@ -49,7 +49,7 @@ LDSHARED=gcc -shared
 #---------------------------------------- End of Unix
 endif
 SHARED_LIBRARIES = $(SHARED:.lib=.so)
-PYREXC=$(shell python -c "import PlatformDependent; print PlatformDependent.find_pyrexc()")
+PYREXC=$(shell python -c "import platform.PlatformDependent; print platform.PlatformDependent.find_pyrexc()")
 CFLAGS+=-fno-strict-aliasing -DNDEBUG -g -Wall -Wmissing-prototypes \
   -Wstrict-prototypes -fPIC
 # These CFLAGS and LDFLAGS are not used by distutils. If asked to
diff --git a/cad/src/GroupButtonMixin.py b/cad/src/PM/GroupButtonMixin.py
index 021a31348..021a31348 100755
--- a/cad/src/GroupButtonMixin.py
+++ b/cad/src/PM/GroupButtonMixin.py
diff --git a/cad/src/PM/PM_CheckBox.py b/cad/src/PM/PM_CheckBox.py
index ba300f6fe..c67aad0d5 100755
--- a/cad/src/PM/PM_CheckBox.py
+++ b/cad/src/PM/PM_CheckBox.py
@@ -20,9 +20,9 @@ from PyQt4.Qt import QWidget
 
 from PM.PM_Constants import pmLeftColumn, pmRightColumn
 
-from prefs_widgets import widget_connectWithState
-from prefs_widgets import QCheckBox_ConnectionWithState
-from prefs_widgets import set_metainfo_from_stateref
+from widgets.prefs_widgets import widget_connectWithState
+from widgets.prefs_widgets import QCheckBox_ConnectionWithState
+from widgets.prefs_widgets import set_metainfo_from_stateref
 
 class PM_CheckBox( QCheckBox ):
     """
diff --git a/cad/src/PM/PM_Clipboard.py b/cad/src/PM/PM_Clipboard.py
index 4b33a2a80..6ec8ff3d7 100644
--- a/cad/src/PM/PM_Clipboard.py
+++ b/cad/src/PM/PM_Clipboard.py
@@ -20,7 +20,7 @@ from PyQt4.Qt import QListWidget
 from PyQt4.Qt import SIGNAL
 from graphics.widgets.ThumbView import MMKitView
 from PM.PM_GroupBox import PM_GroupBox
-from constants      import diTUBES
+from utilities.constants import diTUBES
 
 class PM_Clipboard(PM_GroupBox):     
     """
diff --git a/cad/src/PM/PM_Colors.py b/cad/src/PM/PM_Colors.py
index 1823720ca..735ac9781 100755
--- a/cad/src/PM/PM_Colors.py
+++ b/cad/src/PM/PM_Colors.py
@@ -19,7 +19,7 @@ import sys
 from PyQt4.Qt import QColor
 from PyQt4.Qt import QPalette
 
-from debug_prefs import debug_pref, Choice
+from utilities.debug_prefs import debug_pref, Choice
 
 
 _iconPrefix = os.path.dirname(os.path.abspath(sys.argv[0]))
diff --git a/cad/src/PM/PM_Dialog.py b/cad/src/PM/PM_Dialog.py
index c44567c19..2dd7f5dca 100755
--- a/cad/src/PM/PM_Dialog.py
+++ b/cad/src/PM/PM_Dialog.py
@@ -13,11 +13,11 @@ file and renamed it PM_Dialog.
 
 """
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from utilities import debug_flags
 
-from icon_utilities import geticon
-from icon_utilities import getpixmap
+from utilities.icon_utilities import geticon
+from utilities.icon_utilities import getpixmap
 
 from PyQt4.Qt import Qt
 
@@ -64,7 +64,7 @@ from PyQt4.Qt import QWhatsThis
 from PM.PM_GroupBox         import PM_GroupBox
 from PM.PM_MessageGroupBox  import PM_MessageGroupBox
 
-from Sponsors import SponsorableMixin
+from sponsors.Sponsors import SponsorableMixin
 
 class PM_Dialog( QDialog, SponsorableMixin ):
     """
diff --git a/cad/src/PM/PM_DockWidget.py b/cad/src/PM/PM_DockWidget.py
index 62ed0344e..00f01b787 100644
--- a/cad/src/PM/PM_DockWidget.py
+++ b/cad/src/PM/PM_DockWidget.py
@@ -22,7 +22,7 @@ from PM.PM_Colors    import getPalette
 from PM.PM_Colors import pmGrpBoxColor
 from PM.PM_CheckBox import PM_CheckBox
 from PM.PM_Constants import pmLeftAlignment, pmRightAlignment
-from icon_utilities import getpixmap
+from utilities.icon_utilities import getpixmap
 
 class PM_DockWidget(QDockWidget):
     """
diff --git a/cad/src/PM/PM_DoubleSpinBox.py b/cad/src/PM/PM_DoubleSpinBox.py
index 16d5ef3cd..cbf9836ac 100755
--- a/cad/src/PM/PM_DoubleSpinBox.py
+++ b/cad/src/PM/PM_DoubleSpinBox.py
@@ -16,9 +16,9 @@ from PyQt4.Qt import QDoubleSpinBox
 from PyQt4.Qt import QLabel
 from PyQt4.Qt import QWidget
 
-from prefs_widgets import widget_connectWithState
-from prefs_widgets import QDoubleSpinBox_ConnectionWithState
-from prefs_widgets import set_metainfo_from_stateref
+from widgets.prefs_widgets import widget_connectWithState
+from widgets.prefs_widgets import QDoubleSpinBox_ConnectionWithState
+from widgets.prefs_widgets import set_metainfo_from_stateref
 
 class PM_DoubleSpinBox( QDoubleSpinBox ):
     """
diff --git a/cad/src/PM/PM_GroupBox.py b/cad/src/PM/PM_GroupBox.py
index 1592c0614..6bbfd6815 100755
--- a/cad/src/PM/PM_GroupBox.py
+++ b/cad/src/PM/PM_GroupBox.py
@@ -45,7 +45,7 @@ from PyQt4.Qt import QVBoxLayout
 from PyQt4.Qt import QWidget
 from PyQt4.Qt import SIGNAL
 
-from icon_utilities import geticon, getpixmap
+from utilities.icon_utilities import geticon, getpixmap
 
 #This import is only used in isinstance check--
 from PM.PM_CheckBox import PM_CheckBox
diff --git a/cad/src/PM/PM_ListWidget.py b/cad/src/PM/PM_ListWidget.py
index 8c1c2ef44..e7bfeeae7 100755
--- a/cad/src/PM/PM_ListWidget.py
+++ b/cad/src/PM/PM_ListWidget.py
@@ -16,7 +16,7 @@ from PyQt4.Qt import QLabel
 from PyQt4.Qt import QListWidget
 from PyQt4.Qt import QWidget
 
-from debug     import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 class PM_ListWidget( QListWidget ):
     """
diff --git a/cad/src/PM/PM_MolecularModelingKit.py b/cad/src/PM/PM_MolecularModelingKit.py
index 4c856b0a1..0a6924029 100644
--- a/cad/src/PM/PM_MolecularModelingKit.py
+++ b/cad/src/PM/PM_MolecularModelingKit.py
@@ -12,8 +12,8 @@ from model.elements import PeriodicTable
 from PyQt4.Qt import SIGNAL
 from PM.PM_GroupBox import PM_GroupBox
 from PM.PM_ToolButtonGrid import PM_ToolButtonGrid
-from constants import diTUBES
-from debug import print_compact_traceback
+from utilities.constants import diTUBES
+from utilities.debug import print_compact_traceback
 
 from command_support.GeneratorBaseClass import AbstractMethod
 
diff --git a/cad/src/PM/PM_PAM3_AtomChooser.py b/cad/src/PM/PM_PAM3_AtomChooser.py
index f4c5ded43..c2d8c97d5 100644
--- a/cad/src/PM/PM_PAM3_AtomChooser.py
+++ b/cad/src/PM/PM_PAM3_AtomChooser.py
@@ -9,7 +9,7 @@ PM_PAM3_AtomChooser.py
 """
 
 from PM.PM_MolecularModelingKit import PM_MolecularModelingKit
-from constants import diBALL
+from utilities.constants import diBALL
 
 # Elements button list to create PAM3 atoms toolbutton group.
 # Format: 
diff --git a/cad/src/PM/PM_PAM5_AtomChooser.py b/cad/src/PM/PM_PAM5_AtomChooser.py
index 8e6610eeb..bce824053 100644
--- a/cad/src/PM/PM_PAM5_AtomChooser.py
+++ b/cad/src/PM/PM_PAM5_AtomChooser.py
@@ -10,7 +10,7 @@ PM_PAM5_AtomChooser.py
 
 
 from PM.PM_MolecularModelingKit import PM_MolecularModelingKit
-from constants import diBALL
+from utilities.constants import diBALL
 
 # Elements button list to create PAM5 atoms toolbutton group.
 # Format: 
diff --git a/cad/src/PM/PM_PartLib.py b/cad/src/PM/PM_PartLib.py
index b2bfbd376..de3949534 100644
--- a/cad/src/PM/PM_PartLib.py
+++ b/cad/src/PM/PM_PartLib.py
@@ -21,7 +21,7 @@ ninad 2007-09-06: Created.
 import os
 from utilities import debug_flags
 
-from constants      import diTUBES
+from utilities.constants import diTUBES
 from graphics.widgets.ThumbView import MMKitView
 from model.assembly import assembly
 from files.mmp.files_mmp import readmmp
diff --git a/cad/src/PM/PM_PushButton.py b/cad/src/PM/PM_PushButton.py
index 33d71bc83..0d5bcaade 100755
--- a/cad/src/PM/PM_PushButton.py
+++ b/cad/src/PM/PM_PushButton.py
@@ -16,8 +16,8 @@ from PyQt4.Qt import QLabel
 from PyQt4.Qt import QPushButton
 from PyQt4.Qt import QWidget
 
-from prefs_widgets import widget_setAction
-from prefs_widgets import QPushButton_ConnectionWithAction
+from widgets.prefs_widgets import widget_setAction
+from widgets.prefs_widgets import QPushButton_ConnectionWithAction
 
 class PM_PushButton( QPushButton ):
     """
diff --git a/cad/src/PM/PM_SelectionListWidget.py b/cad/src/PM/PM_SelectionListWidget.py
index 792540b5f..7b4e645ea 100644
--- a/cad/src/PM/PM_SelectionListWidget.py
+++ b/cad/src/PM/PM_SelectionListWidget.py
@@ -53,8 +53,8 @@ from PyQt4.Qt  import QPalette
 from PyQt4.Qt  import QAbstractItemView
 ##from PyQt4.Qt import Qt
 from PM.PM_Colors import getPalette
-from constants import yellow
-from icon_utilities import geticon
+from utilities.constants import yellow
+from utilities.icon_utilities import geticon
 
 TAG_INSTRUCTIONS = ['TAG_ITEM_IN_GLPANE', 
                     'PICK_ITEM_IN_GLPANE',
diff --git a/cad/src/PM/PM_ToolButton.py b/cad/src/PM/PM_ToolButton.py
index 34325291e..c4ce5feb7 100755
--- a/cad/src/PM/PM_ToolButton.py
+++ b/cad/src/PM/PM_ToolButton.py
@@ -18,7 +18,7 @@ from PyQt4.Qt import QToolButton
 from PyQt4.Qt import QWidget
 from PyQt4.Qt import QSize
 
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 class PM_ToolButton( QToolButton ):
     """
diff --git a/cad/src/PM/PM_WidgetGrid.py b/cad/src/PM/PM_WidgetGrid.py
index 1942b115c..f7496186d 100644
--- a/cad/src/PM/PM_WidgetGrid.py
+++ b/cad/src/PM/PM_WidgetGrid.py
@@ -19,8 +19,8 @@ from PyQt4.Qt import QLabel
 from PyQt4.Qt import QToolButton
 from PyQt4.Qt import QPushButton
 
-from debug    import print_compact_traceback
-from icon_utilities import geticon
+from utilities.debug import print_compact_traceback
+from utilities.icon_utilities import geticon
 
 from PM.PM_GroupBox import PM_GroupBox
 
diff --git a/cad/src/PropMgr_Constants.py b/cad/src/PM/PropMgr_Constants.py
index bbbfb7c86..d3b1a9386 100755
--- a/cad/src/PropMgr_Constants.py
+++ b/cad/src/PM/PropMgr_Constants.py
@@ -12,7 +12,7 @@ from PyQt4.Qt import Qt
 from PyQt4.Qt import QColor
 from PyQt4.Qt import QFont
 
-from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False, Choice
+from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False, Choice
 
 __author__ = "Mark"
 
diff --git a/cad/src/analysis/ESP/ESPImage.py b/cad/src/analysis/ESP/ESPImage.py
index 12166898d..a392810be 100755
--- a/cad/src/analysis/ESP/ESPImage.py
+++ b/cad/src/analysis/ESP/ESPImage.py
@@ -76,21 +76,21 @@ from graphics.behaviors.shape import SelectionShape
 from geometry.Slab import Slab
 
 from utilities.Log import redmsg, greenmsg 
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 from model.jigs import Jig # REVIEW: all uses of this are suspicious!
 from graphics.images.ImageUtils import nEImageOps
 
-from constants import black
-from constants import ave_colors
-from constants import green
-from constants import START_NEW_SELECTION
-from constants import SUBTRACT_FROM_SELECTION
+from utilities.constants import black
+from utilities.constants import ave_colors
+from utilities.constants import green
+from utilities.constants import START_NEW_SELECTION
+from utilities.constants import SUBTRACT_FROM_SELECTION
 
 from model.jigs_planes import RectGadget
 from model.jigs_planes import povStrVec
 
 from analysis.ESP.ESPImageProp import ESPImageProp
-from PlatformDependent import find_or_make_Nanorex_subdir
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
 
 from analysis.ESP.NanoHiveUtils import get_nh_espimage_filename
 from analysis.ESP.NanoHiveUtils import run_nh_simulation
@@ -400,7 +400,7 @@ class ESPImage(RectGadget):
         # model space coords.  Mark 050930
         if 0:
             from graphics.drawing.drawer import drawline
-            from constants import yellow
+            from utilities.constants import yellow
             drawline(yellow, self.center, self.center + self.planeNorm, 0, 3)
 
     def writemmp(self, mapping):
diff --git a/cad/src/analysis/ESP/ESPImagePropDialog.py b/cad/src/analysis/ESP/ESPImagePropDialog.py
index e8863654d..9e92f2b9f 100755
--- a/cad/src/analysis/ESP/ESPImagePropDialog.py
+++ b/cad/src/analysis/ESP/ESPImagePropDialog.py
@@ -9,7 +9,7 @@
 # WARNING! All changes made in this file will be lost!
 
 from PyQt4 import QtCore, QtGui
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 class Ui_ESPImagePropDialog(object):
     def setupUi(self, ESPImagePropDialog):
diff --git a/cad/src/analysis/ESP/NanoHive.py b/cad/src/analysis/ESP/NanoHive.py
index d1060f1f0..167b60e71 100755
--- a/cad/src/analysis/ESP/NanoHive.py
+++ b/cad/src/analysis/ESP/NanoHive.py
@@ -17,7 +17,7 @@ from PyQt4.Qt import QString
 
 import foundation.env as env
 
-from constants import filesplit
+from utilities.constants import filesplit
 from utilities.Log import redmsg, greenmsg, orangemsg
 
 from analysis.ESP.NanoHiveDialog import Ui_NanoHiveDialog
diff --git a/cad/src/analysis/ESP/NanoHiveUtils.py b/cad/src/analysis/ESP/NanoHiveUtils.py
index c5f036e73..37d9c5842 100755
--- a/cad/src/analysis/ESP/NanoHiveUtils.py
+++ b/cad/src/analysis/ESP/NanoHiveUtils.py
@@ -18,10 +18,10 @@ Probably "simulation". [bruce 071214]
 """
 
 import foundation.env as env, os, sys, time
-from PlatformDependent import find_or_make_Nanorex_subdir
-from prefs_constants import nanohive_path_prefs_key, nanohive_enabled_prefs_key
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
+from utilities.prefs_constants import nanohive_path_prefs_key, nanohive_enabled_prefs_key
 from PyQt4.Qt import Qt, QApplication, QCursor
-from StatusBar import NanoHiveProgressReporter
+from widgets.StatusBar import NanoHiveProgressReporter
 
 def get_nh_simspec_filename(basename):
     """
@@ -280,7 +280,7 @@ def verify_program(program, version_flag, vstring):
         
     args = [version_flag]
     
-    from Process import Process
+    from processes.Process import Process
     
     arguments = []
     for arg in args:
@@ -332,7 +332,7 @@ def start_nh():
     
     #print "start_nh(): args=", args
     
-    from Process import Process
+    from processes.Process import Process
     
     arguments = []
     for arg in args:
diff --git a/cad/src/analysis/GAMESS/GamessJob.py b/cad/src/analysis/GAMESS/GamessJob.py
index 2640856d3..1d0d8a63b 100755
--- a/cad/src/analysis/GAMESS/GamessJob.py
+++ b/cad/src/analysis/GAMESS/GamessJob.py
@@ -32,22 +32,22 @@ from PyQt4.Qt import SLOT
 from PyQt4.Qt import QThread
 from PyQt4.Qt import QMutex
 
-from SimJob import SimJob
+from simulation.SimJob import SimJob
 from analysis.GAMESS.GamessProp import GamessProp
 from analysis.GAMESS.files_gms import writegms_inpfile
 ## from files_gms import writegms_batfile
 import foundation.preferences as preferences
 import foundation.env as env # for setting prefs and doing recursive event processing
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
-from ServerManager import ServerManager
+from processes.ServerManager import ServerManager
 ## from PlatformDependent import open_file_in_editor
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from ne1_ui.UserPrefs import get_filename_and_save_in_prefs
-from PlatformDependent import hhmmss_str
+from platform.PlatformDependent import hhmmss_str
 
-from prefs_constants import gmspath_prefs_key
-from prefs_constants import gamess_enabled_prefs_key
+from utilities.prefs_constants import gmspath_prefs_key
+from utilities.prefs_constants import gamess_enabled_prefs_key
 
 failpat = re.compile("-ABNORMALLY-")
 irecpat = re.compile(" (\w+) +\d+\.\d* +([\d\.E+-]+) +([\d\.E+-]+) +([\d\.E+-]+)")
diff --git a/cad/src/analysis/GAMESS/GamessProp.py b/cad/src/analysis/GAMESS/GamessProp.py
index d300ea101..74d9d8ec2 100755
--- a/cad/src/analysis/GAMESS/GamessProp.py
+++ b/cad/src/analysis/GAMESS/GamessProp.py
@@ -20,12 +20,12 @@ from PyQt4.Qt import QColorDialog
 import foundation.env as env
 
 from analysis.GAMESS.GamessPropDialog import Ui_GamessPropDialog
-from ServerManager import ServerManager
+from processes.ServerManager import ServerManager
 from utilities.Log import redmsg
 ##from files_gms import insertgms
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from widgets.widget_helpers import RGBf_to_QColor, QColor_to_RGBf, get_widget_with_color_palette
-from qt4transition import qt4todo
+from utilities.qt4transition import qt4todo
 
 
 # Ask Bruce where all this should ultimately live.
@@ -589,7 +589,7 @@ class GamessProp(QDialog, Ui_GamessPropDialog):
         file in an editor.
         '''
         # Make tmp_inputfile filename (i.e. ~/Nanorex/temp/jigname_parms_info.inp)
-        from PlatformDependent import find_or_make_Nanorex_subdir
+        from platform.PlatformDependent import find_or_make_Nanorex_subdir
         tmpdir = find_or_make_Nanorex_subdir('temp')
         basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info('_')
         tmp_inputfile = os.path.join(tmpdir, "%s.inp" % basename)
@@ -598,7 +598,7 @@ class GamessProp(QDialog, Ui_GamessPropDialog):
         from analysis.GAMESS.files_gms import writegms_inpfile
         writegms_inpfile(tmp_inputfile, self.gamessJig)
         
-        from PlatformDependent import open_file_in_editor
+        from platform.PlatformDependent import open_file_in_editor
         open_file_in_editor(tmp_inputfile)
                 
     def run_job(self):
diff --git a/cad/src/analysis/GAMESS/JobManager.py b/cad/src/analysis/GAMESS/JobManager.py
index d24f84048..16a21361e 100755
--- a/cad/src/analysis/GAMESS/JobManager.py
+++ b/cad/src/analysis/GAMESS/JobManager.py
@@ -48,7 +48,7 @@ def touch_job_id_status_file(job_id, Status = 'Queued'):
     """
     
     # Get the Job Manager directory
-    from PlatformDependent import find_or_make_Nanorex_subdir
+    from platform.PlatformDependent import find_or_make_Nanorex_subdir
     jobdir = find_or_make_Nanorex_subdir('JobManager')
     
     # Job Id dir (i.e. ~/Nanorex/JobManager/123/)
@@ -95,7 +95,7 @@ def get_job_manager_job_id_and_dir():
     #    job_id += 1 # Increment the Job Id
     
     # Get the Job Manager directory
-    from PlatformDependent import find_or_make_Nanorex_subdir
+    from platform.PlatformDependent import find_or_make_Nanorex_subdir
     jobdir = find_or_make_Nanorex_subdir('JobManager')
     
     while 1:
@@ -108,7 +108,7 @@ def get_job_manager_job_id_and_dir():
             job_id += 1 # It is there, so increment the Job Id and try again.
             
         else:
-            from debug import print_compact_traceback
+            from utilities.debug import print_compact_traceback
             try:
                 os.mkdir(job_id_dir)
             except:
@@ -247,7 +247,7 @@ class JobManager(QWidget, Ui_JobManagerDialog):
         """
         Scan Job manager directories to find and return all the list of jobs
         """
-        from PlatformDependent import find_or_make_Nanorex_directory
+        from platform.PlatformDependent import find_or_make_Nanorex_directory
         tmpFilePath = find_or_make_Nanorex_directory()
         managerDir = os.path.join(tmpFilePath, "JobManager")
         jobDirs = os.listdir(managerDir)
diff --git a/cad/src/analysis/GAMESS/files_gms.py b/cad/src/analysis/GAMESS/files_gms.py
index e1a03f7a9..1dd78974d 100755
--- a/cad/src/analysis/GAMESS/files_gms.py
+++ b/cad/src/analysis/GAMESS/files_gms.py
@@ -17,7 +17,7 @@ from model.chunk import Chunk
 from model.chem import Atom
 from string import capitalize
 from model.elements import PeriodicTable
-from PlatformDependent import get_gms_name
+from platform.PlatformDependent import get_gms_name
 from utilities.Log import redmsg, orangemsg
 from geometry.VQT import A
 import foundation.env as env
diff --git a/cad/src/analysis/GAMESS/jig_Gamess.py b/cad/src/analysis/GAMESS/jig_Gamess.py
index 17f22d8b8..f3b973b9a 100755
--- a/cad/src/analysis/GAMESS/jig_Gamess.py
+++ b/cad/src/analysis/GAMESS/jig_Gamess.py
@@ -18,7 +18,7 @@ import foundation.env as env
 from utilities.Log import redmsg
 from model.chem import move_alist_and_snuggle
 import foundation.state_utils as state_utils
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from analysis.GAMESS.GamessJob import GamessJob
 from analysis.GAMESS.GamessProp import scftyp
@@ -47,7 +47,7 @@ from analysis.GAMESS.GamessProp import ui
 
 from utilities import debug_flags
 
-from constants import magenta
+from utilities.constants import magenta
 
 from files.mmp.files_mmp_registration import MMP_RecordParser
 from files.mmp.files_mmp_registration import register_MMP_RecordParser
diff --git a/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py b/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py
index 968f984db..de9517b43 100644
--- a/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py
+++ b/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py
@@ -26,7 +26,7 @@ from cnt.model.CntGroup import CntGroup
 from utilities.Log  import greenmsg
 from command_support.GeneratorBaseClass import PluginBug, UserError
 
-from constants import gensym
+from utilities.constants import gensym
 
 from ne1_ui.toolbars.Ui_CntFlyout import CntFlyout
 
diff --git a/cad/src/cnt/commands/BuildCnt/BuildCnt_PropertyManager.py b/cad/src/cnt/commands/BuildCnt/BuildCnt_PropertyManager.py
index 5344b1c3a..d2df30fa1 100644
--- a/cad/src/cnt/commands/BuildCnt/BuildCnt_PropertyManager.py
+++ b/cad/src/cnt/commands/BuildCnt/BuildCnt_PropertyManager.py
@@ -22,7 +22,7 @@ BUGS:
 - Just entering and leaving BuildCnt_EditCommand creates an empty CntGroup
 """
 from utilities import debug_flags
-from debug import  print_compact_stack
+from utilities.debug import print_compact_stack
 
 from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QString
@@ -31,7 +31,7 @@ from PM.PM_GroupBox      import PM_GroupBox
 from PM.PM_PushButton    import PM_PushButton
 from PM.PM_SelectionListWidget import PM_SelectionListWidget
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 
 from PM.PM_Constants     import pmDoneButton
diff --git a/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py b/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py
index 0a1f66ede..945a447f9 100644
--- a/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py
+++ b/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py
@@ -46,18 +46,18 @@ from cnt.commands.InsertCnt.Nanotube import Cnt_Atomistic
 
 from command_support.GeneratorBaseClass import PluginBug, UserError
 
-from constants import gensym
+from utilities.constants import gensym
 
 from cnt.model.Cnt_Constants import getCntLength
-from test_connectWithState import State_preMixin
+from prototype.test_connectWithState import State_preMixin
 
-from constants import noop
+from utilities.constants import noop
 from exprs.attr_decl_macros import Instance, State
 
 from exprs.__Symbols__ import _self
 from exprs.Exprs import call_Expr
 from exprs.Exprs import norm_Expr
-from prefs_widgets import ObjAttr_StateRef
+from widgets.prefs_widgets import ObjAttr_StateRef
 from exprs.ExprsConstants import Width, Point
 
 from model.chunk import Chunk
diff --git a/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py b/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py
index 7ada4feed..7ff338ca0 100644
--- a/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py
+++ b/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py
@@ -39,7 +39,7 @@ from cnt.commands.BuildCnt.BuildCnt_GraphicsMode import BuildCnt_GraphicsMode
 from cnt.model.CntSegment import CntSegment
 
 from cnt.temporary_commands.CntLineMode import CntLine_GM
-from TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
+from temporary_commands.TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
 
 from graphics.drawing.drawCntLadder import drawCntLadder
 
@@ -47,8 +47,8 @@ import foundation.env as env
 
 import math
 from geometry.VQT import V, norm, A, Q, vlen
-from constants import darkred, blue, black
-from debug import print_compact_traceback
+from utilities.constants import darkred, blue, black
+from utilities.debug import print_compact_traceback
 
 from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT
 
diff --git a/cad/src/cnt/commands/CntSegment/CntSegment_PropertyManager.py b/cad/src/cnt/commands/CntSegment/CntSegment_PropertyManager.py
index dfe6b68ee..d56692e64 100644
--- a/cad/src/cnt/commands/CntSegment/CntSegment_PropertyManager.py
+++ b/cad/src/cnt/commands/CntSegment/CntSegment_PropertyManager.py
@@ -10,7 +10,7 @@ See CntSegment_EditCommand for details.
 from PyQt4.Qt import SIGNAL
 from PM.PM_GroupBox      import PM_GroupBox
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 
 from PM.PM_Constants     import pmDoneButton
diff --git a/cad/src/cnt/commands/CntSegment/CntSegment_ResizeHandle.py b/cad/src/cnt/commands/CntSegment/CntSegment_ResizeHandle.py
index d29b4a1e0..936665c33 100644
--- a/cad/src/cnt/commands/CntSegment/CntSegment_ResizeHandle.py
+++ b/cad/src/cnt/commands/CntSegment/CntSegment_ResizeHandle.py
@@ -24,8 +24,8 @@ from exprs.Rect             import Sphere
 
 from exprs.Arrow import Arrow
    
-from constants  import yellow, darkgreen
-from constants  import olive
+from utilities.constants import yellow, darkgreen
+from utilities.constants import olive
 
 from geometry.VQT import V
 from exprs.DraggableHandle import DraggableHandle_AlongLine
diff --git a/cad/src/cnt/commands/InsertCnt/InsertCnt_EditCommand.py b/cad/src/cnt/commands/InsertCnt/InsertCnt_EditCommand.py
index cb694df3c..6fa314bfa 100644
--- a/cad/src/cnt/commands/InsertCnt/InsertCnt_EditCommand.py
+++ b/cad/src/cnt/commands/InsertCnt/InsertCnt_EditCommand.py
@@ -29,7 +29,7 @@ from command_support.EditCommand import EditCommand
 
 from cnt.model.CntSegment import CntSegment
 from cnt.model.CntGroup import CntGroup
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 from utilities.Log  import redmsg, greenmsg
 from geometry.VQT import V, Veq, vlen
@@ -39,7 +39,7 @@ from cnt.commands.InsertCnt.Nanotube import Cnt_Atomistic
 from command_support.GeneratorBaseClass import PluginBug, UserError
 from cnt.commands.InsertCnt.InsertCnt_PropertyManager import InsertCnt_PropertyManager
 
-from constants import gensym
+from utilities.constants import gensym
 
 from cnt.model.Cnt_Constants import getNumberOfCellsFromCntLength
 from cnt.model.Cnt_Constants import getCntLength
diff --git a/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py b/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py
index 6a83f3e00..5d46ff0b0 100644
--- a/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py
+++ b/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py
@@ -31,7 +31,7 @@ from PM.PM_ToolButton    import PM_ToolButton
 from PM.PM_CoordinateSpinBoxes import PM_CoordinateSpinBoxes
 from PM.PM_CheckBox   import PM_CheckBox
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 from geometry.VQT import V
 
diff --git a/cad/src/cnt/commands/InsertCnt/Nanotube.py b/cad/src/cnt/commands/InsertCnt/Nanotube.py
index 8a49dd138..6e185ab1f 100644
--- a/cad/src/cnt/commands/InsertCnt/Nanotube.py
+++ b/cad/src/cnt/commands/InsertCnt/Nanotube.py
@@ -17,15 +17,15 @@ import os
 
 from math    import sin, cos, pi
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from PlatformDependent  import find_plugin_dir
+from platform.PlatformDependent import find_plugin_dir
 from files.mmp.files_mmp import readmmp
 from geometry.VQT import Q, V, angleBetween, cross, vlen
 from commands.Fuse.fusechunksMode import fusechunksBase
 from utilities.Log      import orangemsg
 from command_support.GeneratorBaseClass import PluginBug
-from prefs_constants import dnaDefaultSegmentColor_prefs_key
+from utilities.prefs_constants import dnaDefaultSegmentColor_prefs_key
 
 basepath_ok, basepath = find_plugin_dir("Nanotube")
 if not basepath_ok:
diff --git a/cad/src/cnt/model/CntGroup.py b/cad/src/cnt/model/CntGroup.py
index 4ac8e3ba8..72771933a 100644
--- a/cad/src/cnt/model/CntGroup.py
+++ b/cad/src/cnt/model/CntGroup.py
@@ -10,9 +10,9 @@ CntGroup.py - ...
 from dna.model.Block import Block
 from model.chunk import Chunk
 
-from constants import gensym
+from utilities.constants import gensym
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 from cnt.updater.cnt_updater_globals import _f_CntGroup_for_homeless_objects_in_Part
 
diff --git a/cad/src/cnt/model/CntLadderRailChunk.py b/cad/src/cnt/model/CntLadderRailChunk.py
index 193cc1ce7..a3b3bb8de 100644
--- a/cad/src/cnt/model/CntLadderRailChunk.py
+++ b/cad/src/cnt/model/CntLadderRailChunk.py
@@ -9,10 +9,10 @@ CntLadderRailChunk.py -
 
 from model.chunk import Chunk
 
-from constants import gensym
-from constants import black
-from constants import ave_colors
-from constants import diDEFAULT
+from utilities.constants import gensym
+from utilities.constants import black
+from utilities.constants import ave_colors
+from utilities.constants import diDEFAULT
 
 from utilities import debug_flags
 
diff --git a/cad/src/cnt/model/CntSegment.py b/cad/src/cnt/model/CntSegment.py
index d49ae8c9a..e23b074e3 100644
--- a/cad/src/cnt/model/CntSegment.py
+++ b/cad/src/cnt/model/CntSegment.py
@@ -10,7 +10,7 @@ import foundation.env as env
 from cnt.model.CntStrandOrSegment import CntStrandOrSegment
 from cnt.model.CntLadderRailChunk import CntAxisChunk
 
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 from model.chunk import Chunk
 from model.chem import Atom
 from model.bonds import Bond
diff --git a/cad/src/cnt/temporary_commands/CntLineMode.py b/cad/src/cnt/temporary_commands/CntLineMode.py
index 8e8249716..ec4dc65ba 100644
--- a/cad/src/cnt/temporary_commands/CntLineMode.py
+++ b/cad/src/cnt/temporary_commands/CntLineMode.py
@@ -9,11 +9,11 @@ TODO:
 - User Preferences for different rubberband line display styles 
 """
 
-from LineMode import LineMode
+from temporary_commands.LineMode import LineMode
 
 from graphics.drawing.drawCntLadder import drawCntLadder
 
-from constants import gray, black, darkred, blue, white
+from utilities.constants import gray, black, darkred, blue, white
 
 # == GraphicsMode part
 
diff --git a/cad/src/cnt/updater/cnt_updater_globals.py b/cad/src/cnt/updater/cnt_updater_globals.py
index 6b433837a..636cd934d 100644
--- a/cad/src/cnt/updater/cnt_updater_globals.py
+++ b/cad/src/cnt/updater/cnt_updater_globals.py
@@ -15,7 +15,7 @@ from foundation.changedicts import _cdproc_for_dictid # but it's private!
 
 from model.chem import _changed_structure_Atoms, _changed_parent_Atoms # but they're private! refactor sometime
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 _DEBUG_ATOM_KEY = None # None, or a value of atom.key for which all ignored changes should be printed
 
diff --git a/cad/src/commandSequencer/CommandSequencer.py b/cad/src/commandSequencer/CommandSequencer.py
index 879ec2635..aeee2f49c 100644
--- a/cad/src/commandSequencer/CommandSequencer.py
+++ b/cad/src/commandSequencer/CommandSequencer.py
@@ -28,7 +28,7 @@ in basicMode is really part of the command sequencer (which basicMode should jus
 interface to rather than "try to be").
 """
 
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 from utilities import debug_flags
 import foundation.env as env
 import os
@@ -660,7 +660,7 @@ class modeMixin(object):
         res = []
         try:
             # special case for cad/src/exprs/testmode.py (or .pyc)
-            from constants import CAD_SRC_PATH
+            from utilities.constants import CAD_SRC_PATH
             ## CAD_SRC_PATH = os.path.dirname(__file__)
             for filename in ('testmode.py', 'testmode.pyc'):
                 testmodefile = os.path.join( CAD_SRC_PATH, "exprs", filename)
@@ -679,7 +679,7 @@ class modeMixin(object):
                 print "fyi: error adding testmode.py from cad/src/exprs to custom modes menu (ignored)"
             pass
         try:
-            import gpl_only
+            import platform.gpl_only as gpl_only
         except ImportError:
             pass
         else:
@@ -722,7 +722,7 @@ class modeMixin(object):
                     # we'll load it from there instead. That's basically a bug,
                     # but prepending dir onto path would risk much worse bugs
                     # if dir masked any standard modules which got loaded now.
-            import gpl_only # make sure exec is ok in this version (caller should have done this already)
+            import platform.gpl_only as gpl_only # make sure exec is ok in this version (caller should have done this already)
             _module = _modeclass = None # fool pylint into realizing this is not undefined 2 lines below
             exec("import %s as _module" % (base,))
             reload(_module)
diff --git a/cad/src/commandSequencer/builtin_command_loaders.py b/cad/src/commandSequencer/builtin_command_loaders.py
index 63c4d4274..885f35faf 100644
--- a/cad/src/commandSequencer/builtin_command_loaders.py
+++ b/cad/src/commandSequencer/builtin_command_loaders.py
@@ -35,11 +35,11 @@ from commands.Extrude.extrudeMode import extrudeMode
 from commands.Paste.PasteMode import PasteMode
 from commands.PartLibrary.PartLibraryMode import PartLibraryMode
 from commands.PlayMovie.movieMode import movieMode
-from ZoomToAreaMode  import ZoomToAreaMode
-from ZoomInOutMode   import ZoomInOutMode
-from PanMode         import PanMode
-from RotateMode      import RotateMode
-from LineMode        import LineMode
+from temporary_commands.ZoomToAreaMode import ZoomToAreaMode
+from temporary_commands.ZoomInOutMode import ZoomInOutMode
+from temporary_commands.PanMode import PanMode
+from temporary_commands.RotateMode import RotateMode
+from temporary_commands.LineMode import LineMode
 from dna.temporary_commands.DnaLineMode import DnaLineMode
 from dna.commands.BuildDuplex.DnaDuplex_EditCommand import DnaDuplex_EditCommand
 from commands.PlaneProperties.Plane_EditCommand import Plane_EditCommand
diff --git a/cad/src/commandToolbar/CommandToolbar.py b/cad/src/commandToolbar/CommandToolbar.py
index d1383c5ad..3e231be09 100755
--- a/cad/src/commandToolbar/CommandToolbar.py
+++ b/cad/src/commandToolbar/CommandToolbar.py
@@ -82,7 +82,7 @@ from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QToolButton
 
 from ne1_ui.toolbars.Ui_CommandToolbar import Ui_CommandToolbar
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 class CommandToolbar(Ui_CommandToolbar):
     """
diff --git a/cad/src/command_support/Command.py b/cad/src/command_support/Command.py
index cc7a8d7b9..d0ecc08b1 100755
--- a/cad/src/command_support/Command.py
+++ b/cad/src/command_support/Command.py
@@ -27,19 +27,19 @@ basicCommand._exitMode and CommandSequencer.start_using_mode need cleanup.
 
 from PyQt4.Qt import QToolButton
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from debug_prefs import debug_pref, Choice_boolean_False ##, Choice_boolean_True
+from utilities.debug_prefs import debug_pref, Choice_boolean_False ##, Choice_boolean_True
 
 from utilities import debug_flags
-from PlatformDependent import shift_name
-from PlatformDependent import control_name
-from PlatformDependent import context_menu_prefix
+from platform.PlatformDependent import shift_name
+from platform.PlatformDependent import control_name
+from platform.PlatformDependent import context_menu_prefix
 
 import foundation.env as env
 from foundation.state_utils import StateMixin
 
-from constants import noop, GLPANE_IS_COMMAND_SEQUENCER
+from utilities.constants import noop, GLPANE_IS_COMMAND_SEQUENCER
 
 from model.jigs import Jig
     # this is used only for cmenu making
diff --git a/cad/src/command_support/EditCommand.py b/cad/src/command_support/EditCommand.py
index c68f341ae..64c2d0d6a 100644
--- a/cad/src/command_support/EditCommand.py
+++ b/cad/src/command_support/EditCommand.py
@@ -36,7 +36,7 @@ TODO:
 import foundation.changes as changes
 from utilities.Comparison import same_vals
 
-from constants            import permit_gensym_to_reuse_name
+from utilities.constants import permit_gensym_to_reuse_name
 from command_support.GeneratorBaseClass import AbstractMethod
 
 from commands.Select.Select_Command import Select_Command
diff --git a/cad/src/command_support/EditCommand_PM.py b/cad/src/command_support/EditCommand_PM.py
index a5416528c..0db43e92b 100644
--- a/cad/src/command_support/EditCommand_PM.py
+++ b/cad/src/command_support/EditCommand_PM.py
@@ -18,7 +18,7 @@ from PyQt4.Qt import QWidgetAction
 from PyQt4.Qt import SIGNAL
 
 from command_support.GeneratorBaseClass import AbstractMethod
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 class EditCommand_PM(PM_Dialog):
     """    
diff --git a/cad/src/command_support/GeneratorBaseClass.py b/cad/src/command_support/GeneratorBaseClass.py
index 714a4ebd4..3a267a6c0 100755
--- a/cad/src/command_support/GeneratorBaseClass.py
+++ b/cad/src/command_support/GeneratorBaseClass.py
@@ -64,9 +64,9 @@ from utilities import debug_flags
 
 from utilities.Log import redmsg, orangemsg, greenmsg, quote_html
 from utilities.Comparison import same_vals
-from debug import print_compact_traceback
-from constants import gensym
-from constants import permit_gensym_to_reuse_name
+from utilities.debug import print_compact_traceback
+from utilities.constants import gensym
+from utilities.constants import permit_gensym_to_reuse_name
 
 # == private definitions
 
diff --git a/cad/src/command_support/GraphicsMode.py b/cad/src/command_support/GraphicsMode.py
index d0a992e60..7767c1bf6 100755
--- a/cad/src/command_support/GraphicsMode.py
+++ b/cad/src/command_support/GraphicsMode.py
@@ -31,20 +31,20 @@ from PyQt4.Qt import QMenu
 from geometry.VQT import V, Q, vlen, norm, planeXline, ptonline, cross
 import graphics.drawing.drawer as drawer
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from utilities import debug_flags
 
 import foundation.env as env
 from graphics.behaviors.shape import get_selCurve_color
 
-from constants import SELSHAPE_RECT
-from constants import yellow
+from utilities.constants import SELSHAPE_RECT
+from utilities.constants import yellow
 
-from prefs_constants import zoomAboutScreenCenter_prefs_key
-from prefs_constants import displayOriginAxis_prefs_key
-from prefs_constants import displayOriginAsSmallAxis_prefs_key
-from prefs_constants import displayPOVAxis_prefs_key
+from utilities.prefs_constants import zoomAboutScreenCenter_prefs_key
+from utilities.prefs_constants import displayOriginAxis_prefs_key
+from utilities.prefs_constants import displayOriginAsSmallAxis_prefs_key
+from utilities.prefs_constants import displayPOVAxis_prefs_key
 
 from model.chem import Atom
 from model.bonds import Bond
@@ -237,7 +237,7 @@ class basicGraphicsMode(GraphicsMode_API):
         [part of GLPane's drawing interface to modes]
         """
         # conf corner is enabled by default for A9.1 (070627); requires exprs module and Python Imaging Library
-        from debug_prefs import debug_pref, Choice_boolean_True
+        from utilities.debug_prefs import debug_pref, Choice_boolean_True
         if not debug_pref("Enable confirmation corner?", Choice_boolean_True, prefs_key = True):
             return 
         # figure out what kind of confirmation corner we want, and draw it
@@ -876,7 +876,7 @@ class basicGraphicsMode(GraphicsMode_API):
                 # (Old behavior was to use the same pref as for zooming in.)
                 #e [Should this be a separate user pref? For now it's a debug pref, just for testing.
                 #   We might replace these two prefs with a 3-choice pref which controls them both.]
-                from debug_prefs import debug_pref, Choice_boolean_False
+                from utilities.debug_prefs import debug_pref, Choice_boolean_False
                 if debug_pref("GLPane: zoom out acts the same as zoom in?", Choice_boolean_False,
                               prefs_key = "A9 devel/GLPane: zoom out same as zoom in?"
                               ):
diff --git a/cad/src/command_support/JigProp.py b/cad/src/command_support/JigProp.py
index 365d69e24..e3ef5ff3e 100755
--- a/cad/src/command_support/JigProp.py
+++ b/cad/src/command_support/JigProp.py
@@ -13,7 +13,7 @@ __author__ = "Mark"
 from PyQt4.Qt import QDialog
 from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QColorDialog
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 from command_support.JigPropDialog import Ui_JigPropDialog
 
diff --git a/cad/src/command_support/MotorPropertyManager.py b/cad/src/command_support/MotorPropertyManager.py
index be65e6737..e53ac606a 100644
--- a/cad/src/command_support/MotorPropertyManager.py
+++ b/cad/src/command_support/MotorPropertyManager.py
@@ -19,7 +19,7 @@ from command_support.GeneratorBaseClass import AbstractMethod
 from command_support.EditCommand_PM import EditCommand_PM
 
 
-from debug               import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 class MotorPropertyManager(EditCommand_PM):
     """
diff --git a/cad/src/command_support/ParameterDialog.py b/cad/src/command_support/ParameterDialog.py
index fba31e4da..4a5c4bec8 100755
--- a/cad/src/command_support/ParameterDialog.py
+++ b/cad/src/command_support/ParameterDialog.py
@@ -48,18 +48,18 @@ from PyQt4.Qt import SLOT
 
 from command_support.generator_button_images import image0_data, image1_data, image2_data, image3_data, image4_data, image5_data, image6_data, image7_data
 
-from widget_controllers import CollapsibleGroupController_Qt, FloatLineeditController_Qt #e might be gotten from env instead...
+from widgets.widget_controllers import CollapsibleGroupController_Qt, FloatLineeditController_Qt #e might be gotten from env instead...
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from qt4transition import qt4todo
+from utilities.qt4transition import qt4todo
 
 import foundation.env as env # for env.debug(); warning: some methods have a local variable which overrides this
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 from tokenize import generate_tokens #bruce 080101 moved to toplevel, untested
-from parse_utils import parse_top, Whole #bruce 080101 moved to toplevel, untested
+from utilities.parse_utils import parse_top, Whole #bruce 080101 moved to toplevel, untested
 
 
 # image uses -- we should rename them ####@@@@
diff --git a/cad/src/command_support/modes.py b/cad/src/command_support/modes.py
index 603c42661..bfdd9698c 100755
--- a/cad/src/command_support/modes.py
+++ b/cad/src/command_support/modes.py
@@ -53,7 +53,7 @@ even though it can't yet replace the ones it splits out of.
 since those are all split now.]
 """
 
-from constants import GLPANE_IS_COMMAND_SEQUENCER
+from utilities.constants import GLPANE_IS_COMMAND_SEQUENCER
 
 from command_support.Command import anyCommand, nullCommand, basicCommand
 
diff --git a/cad/src/commands/BuildAtom/AtomGeneratorPropertyManager.py b/cad/src/commands/BuildAtom/AtomGeneratorPropertyManager.py
index 8c9c28dc0..218b7b73f 100755
--- a/cad/src/commands/BuildAtom/AtomGeneratorPropertyManager.py
+++ b/cad/src/commands/BuildAtom/AtomGeneratorPropertyManager.py
@@ -48,7 +48,7 @@ History:
   
 """
 
-from icon_utilities import geticon, getpixmap
+from utilities.icon_utilities import geticon, getpixmap
 
 from PyQt4.Qt import Qt, SIGNAL
 
diff --git a/cad/src/commands/BuildAtoms/BuildAtoms_Command.py b/cad/src/commands/BuildAtoms/BuildAtoms_Command.py
index 1e6bc0ae6..b1035e5f2 100755
--- a/cad/src/commands/BuildAtoms/BuildAtoms_Command.py
+++ b/cad/src/commands/BuildAtoms/BuildAtoms_Command.py
@@ -40,13 +40,13 @@ from PyQt4.Qt import SIGNAL
 import foundation.env as env
 import foundation.changes as changes
 
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
-from debug import print_compact_stack
-from debug import print_compact_traceback
+from utilities.debug import print_compact_stack
+from utilities.debug import print_compact_traceback
 
-from prefs_constants import buildModeHighlightingEnabled_prefs_key
-from prefs_constants import keepBondsDuringTransmute_prefs_key
+from utilities.prefs_constants import buildModeHighlightingEnabled_prefs_key
+from utilities.prefs_constants import keepBondsDuringTransmute_prefs_key
 
 from commands.BuildAtoms.BuildAtomsPropertyManager import BuildAtomsPropertyManager
 from commands.SelectAtoms.SelectAtoms_Command import SelectAtoms_basicCommand
diff --git a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
index 8da6ac18c..17a59cbec 100755
--- a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
+++ b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
@@ -59,7 +59,7 @@ from PyQt4.Qt import Qt
 import foundation.env as env
 from utilities import debug_flags
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
 from model.chunk import Chunk
 from model.chem import Atom
@@ -77,11 +77,11 @@ from graphics.behaviors.shape import get_selCurve_color
 from model.bonds import bond_atoms, bond_at_singlets
 from model.bond_constants import V_SINGLE
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
-from constants import elemKeyTab
-from constants import diINVISIBLE
-from constants import diTUBES
+from utilities.constants import elemKeyTab
+from utilities.constants import diINVISIBLE
+from utilities.constants import diTUBES
 
 from model.bond_constants import btype_from_v6
 from model.bond_constants import V_DOUBLE
@@ -89,8 +89,8 @@ from model.bond_constants import V_GRAPHITE
 from model.bond_constants import V_TRIPLE
 from model.bond_constants import V_AROMATIC
 
-from prefs_constants import buildModeSelectAtomsOfDepositedObjEnabled_prefs_key
-from prefs_constants import buildModeWaterEnabled_prefs_key
+from utilities.prefs_constants import buildModeSelectAtomsOfDepositedObjEnabled_prefs_key
+from utilities.prefs_constants import buildModeWaterEnabled_prefs_key
 
 from utilities.Log import orangemsg, redmsg
 
@@ -269,7 +269,7 @@ class BuildAtoms_basicGraphicsMode(SelectAtoms_basicGraphicsMode):
         if v6 is not None:
             self.set_cmdname('Change Bond')
             btype = btype_from_v6( v6)
-            from bond_utils import apply_btype_to_bond
+            from operations.bond_utils import apply_btype_to_bond
             
             apply_btype_to_bond( 
                 btype, 
diff --git a/cad/src/commands/BuildAtoms/build_utils.py b/cad/src/commands/BuildAtoms/build_utils.py
index dca03f9aa..014ddd397 100755
--- a/cad/src/commands/BuildAtoms/build_utils.py
+++ b/cad/src/commands/BuildAtoms/build_utils.py
@@ -19,7 +19,7 @@ with new bonding patterns. And did some of that extension, 050511.
 from geometry.VQT import norm
 from model.chem import Atom
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 class DepositionTool:
     "#doc"
@@ -154,7 +154,7 @@ class AtomTypeDepositionTool(DepositionTool):
                 msg = " (%d bond(s) made)" % n
             else:
                 msg = " (%d bond(s) NOT made, since autobond is off)" % (n-1) #bruce 050901 new feature
-            from PlatformDependent import fix_plurals
+            from platform.PlatformDependent import fix_plurals
             msg = fix_plurals(msg)
             desc += msg
         return atm, desc
diff --git a/cad/src/commands/BuildAtoms/depositMode.py b/cad/src/commands/BuildAtoms/depositMode.py
index 02a5c4a95..5205156c8 100755
--- a/cad/src/commands/BuildAtoms/depositMode.py
+++ b/cad/src/commands/BuildAtoms/depositMode.py
@@ -18,8 +18,8 @@ GraphicsMode parts and the these classes were moved into their own module
 [ See BuildAtoms_Command.py and BuildAtoms_GraphicsMode.py]
 """
 
-from debug import print_compact_traceback
-from constants import GLPANE_IS_COMMAND_SEQUENCER
+from utilities.debug import print_compact_traceback
+from utilities.constants import GLPANE_IS_COMMAND_SEQUENCER
 
 from commands.BuildAtoms.BuildAtoms_Command import BuildAtoms_basicCommand
 from commands.BuildAtoms.BuildAtoms_GraphicsMode import BuildAtoms_basicGraphicsMode
diff --git a/cad/src/commands/BuildCrystal/CookieCtrlPanel.py b/cad/src/commands/BuildCrystal/CookieCtrlPanel.py
index 8dadf4090..90810a874 100755
--- a/cad/src/commands/BuildCrystal/CookieCtrlPanel.py
+++ b/cad/src/commands/BuildCrystal/CookieCtrlPanel.py
@@ -21,8 +21,8 @@ from PyQt4.Qt import QColor
 from PyQt4.Qt import QColorDialog
 
 from commands.BuildCrystal.CookiePropertyManager import CookiePropertyManager
-from icon_utilities import geticon
-from constants import dispLabel
+from utilities.icon_utilities import geticon
+from utilities.constants import dispLabel
 
 
 class CookieCtrlPanel(CookiePropertyManager):
diff --git a/cad/src/commands/BuildCrystal/CookieShape.py b/cad/src/commands/BuildCrystal/CookieShape.py
index 6262a8d5c..df29dedc6 100755
--- a/cad/src/commands/BuildCrystal/CookieShape.py
+++ b/cad/src/commands/BuildCrystal/CookieShape.py
@@ -33,13 +33,13 @@ from graphics.drawing.drawer import drawsphere
 from graphics.drawing.drawer import drawline
 from graphics.drawing.drawer import ColorSorter, ColorSortedDisplayList
 
-from constants import SUBTRACT_FROM_SELECTION
-from constants import OUTSIDE_SUBTRACT_FROM_SELECTION
-from constants import ADD_TO_SELECTION
-from constants import START_NEW_SELECTION
-from constants import white
+from utilities.constants import SUBTRACT_FROM_SELECTION
+from utilities.constants import OUTSIDE_SUBTRACT_FROM_SELECTION
+from utilities.constants import ADD_TO_SELECTION
+from utilities.constants import START_NEW_SELECTION
+from utilities.constants import white
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from geometry.BoundingBox import BBox
 
@@ -850,7 +850,7 @@ class CookieShape(shape):
         """
         from model.chunk import Chunk
         from model.chem import Atom
-        from constants import gensym
+        from utilities.constants import gensym
         
         numLayers = len(self.bondLayers)
         if numLayers:
diff --git a/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py b/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py
index a5d3e1489..9d43c4a36 100755
--- a/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py
+++ b/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py
@@ -33,7 +33,7 @@ from PM.PM_Constants     import pmDoneButton
 from PM.PM_Constants     import pmWhatsThisButton
 from PM.PM_Constants     import pmCancelButton
 
-from icon_utilities      import geticon
+from utilities.icon_utilities import geticon
 
 __author__ = "Ninad"
 
diff --git a/cad/src/commands/BuildCrystal/cookieMode.py b/cad/src/commands/BuildCrystal/cookieMode.py
index bfdf7c8f6..1b8e6f76d 100755
--- a/cad/src/commands/BuildCrystal/cookieMode.py
+++ b/cad/src/commands/BuildCrystal/cookieMode.py
@@ -48,14 +48,14 @@ from graphics.drawing.drawer import genDiam
 from model.chunk import Chunk
 from model.chem import Atom
 
-from constants import gensym
-from constants import diTUBES
-from constants import SELSHAPE_LASSO
-from constants import START_NEW_SELECTION
-from constants import white
-from constants import ADD_TO_SELECTION
-from constants import SUBTRACT_FROM_SELECTION
-from constants import SELSHAPE_RECT
+from utilities.constants import gensym
+from utilities.constants import diTUBES
+from utilities.constants import SELSHAPE_LASSO
+from utilities.constants import START_NEW_SELECTION
+from utilities.constants import white
+from utilities.constants import ADD_TO_SELECTION
+from utilities.constants import SUBTRACT_FROM_SELECTION
+from utilities.constants import SELSHAPE_RECT
 
 import foundation.changes as changes
 
diff --git a/cad/src/commands/CommentProperties/CommentProp.py b/cad/src/commands/CommentProperties/CommentProp.py
index 99ca76fda..bf4ad455e 100755
--- a/cad/src/commands/CommentProperties/CommentProp.py
+++ b/cad/src/commands/CommentProperties/CommentProp.py
@@ -18,8 +18,8 @@ from commands.CommentProperties.CommentPropDialog import Ui_CommentPropDialog
 import time
 import foundation.env as env
 from utilities.Log import redmsg, orangemsg, greenmsg, quote_html
-from qt4transition import qt4todo
-from debug import print_compact_traceback
+from utilities.qt4transition import qt4todo
+from utilities.debug import print_compact_traceback
 
 cmd = greenmsg("Insert Comment: ")
 
diff --git a/cad/src/commands/ElementColors/elementColors.py b/cad/src/commands/ElementColors/elementColors.py
index a649f476a..c020231ef 100755
--- a/cad/src/commands/ElementColors/elementColors.py
+++ b/cad/src/commands/ElementColors/elementColors.py
@@ -16,9 +16,9 @@ from PyQt4.Qt import QGLFormat
 
 from commands.ElementColors.ElementColorsDialog import Ui_ElementColorsDialog
 from model.elements import PeriodicTable 
-from constants import diTrueCPK, diBALL, diTUBES 
+from utilities.constants import diTrueCPK, diBALL, diTUBES 
 from graphics.widgets.ThumbView import ElementView
-from qt4transition import qt4todo
+from utilities.qt4transition import qt4todo
 
 from utilities.Log import redmsg # Mark 050311
 from geometry.VQT import V
@@ -214,7 +214,7 @@ class elementColors(QDialog, Ui_ElementColorsDialog):
         if self.w.assy.filename: 
             odir = os.path.dirname(self.w.assy.filename)
         else: 
-            from prefs_constants import workingDirectory_prefs_key
+            from utilities.prefs_constants import workingDirectory_prefs_key
             odir = env.prefs[workingDirectory_prefs_key]
         self.fileName = str( QFileDialog.getOpenFileName(
                                 self,
@@ -246,7 +246,7 @@ class elementColors(QDialog, Ui_ElementColorsDialog):
         currently only r,g,b color of each element will be saved.
         """
         if not self.fileName:
-           from prefs_constants import workingDirectory_prefs_key   
+           from utilities.prefs_constants import workingDirectory_prefs_key   
            sdir = env.prefs[workingDirectory_prefs_key]
         else:
            sdir = self.fileName
diff --git a/cad/src/commands/ElementSelector/elementSelector.py b/cad/src/commands/ElementSelector/elementSelector.py
index 8246e1b42..1ed97b543 100755
--- a/cad/src/commands/ElementSelector/elementSelector.py
+++ b/cad/src/commands/ElementSelector/elementSelector.py
@@ -12,7 +12,7 @@ from PyQt4.Qt import QVBoxLayout
 from commands.ElementSelector.ElementSelectorDialog import Ui_ElementSelectorDialog
 from graphics.widgets.ThumbView import ElementView
 from model.elements import PeriodicTable
-from constants import diTUBES
+from utilities.constants import diTUBES
 
 class elementSelector(QDialog, Ui_ElementSelectorDialog):
     def __init__(self, win):
diff --git a/cad/src/commands/Extrude/extrudeMode.py b/cad/src/commands/Extrude/extrudeMode.py
index 97069a899..19521a24e 100755
--- a/cad/src/commands/Extrude/extrudeMode.py
+++ b/cad/src/commands/Extrude/extrudeMode.py
@@ -48,12 +48,12 @@ from PyQt4.Qt import Qt
 from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QCursor
 
-from debug_prefs import debug_pref, Choice, Choice_boolean_False ##, Choice_boolean_True
+from utilities.debug_prefs import debug_pref, Choice, Choice_boolean_False ##, Choice_boolean_True
 
 from command_support.modes import basicMode
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 from model.bonds import bond_at_singlets
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from utilities.Log import redmsg
 
 from geometry.VQT import check_posns_near, check_quats_near
@@ -69,8 +69,8 @@ from graphics.behaviors.shape import get_selCurve_color
 from graphics.drawables.handles import repunitHandleSet
 from graphics.drawables.handles import niceoffsetsHandleSet
 from graphics.drawables.handles import draggableHandle_HandleSet
-from constants import blue
-from constants import green
+from utilities.constants import blue
+from utilities.constants import green
 
 MAX_NCOPIES = 360 # max number of extrude-unit copies. Should this be larger? Motivation is to avoid "hangs from slowness".
 
@@ -1602,7 +1602,7 @@ class extrudeMode(basicMode):
                       Choice_boolean_False, prefs_key = True ): #bruce 070928
             if self.product_type == 'closed ring':
                 try:
-                    from constants import red
+                    from utilities.constants import red
                     self.update_ring_geometry(emit_messages = False)
                         # emit_messages = False to fix infinite redraw loop
                         # when it chooses z-y plane and prints a message about that
@@ -2107,7 +2107,7 @@ class fake_merged_mol( virtual_group_of_Chunks): #e rename? 'extrude_unit_holder
         # WARNING: the following code after our call to copy_nodes_in_order is similar to
         # other code after calls to the related function copied_nodes_for_DND, e.g. in depositMode.py.
         # A higher-level utility routine which does all this post-processing should be added to ops_copy.py. ###e
-        from ops_copy import copy_nodes_in_order
+        from operations.ops_copy import copy_nodes_in_order
             #bruce 070525 precaution: use this instead of copied_nodes_for_DND, since order
             # (in fact, precise 1-1 orig-copy correspondence) matters here.
         oldnodes = self._mols
diff --git a/cad/src/commands/Fuse/FuseChunks_Command.py b/cad/src/commands/Fuse/FuseChunks_Command.py
index c5d50f64d..d08375225 100755
--- a/cad/src/commands/Fuse/FuseChunks_Command.py
+++ b/cad/src/commands/Fuse/FuseChunks_Command.py
@@ -24,10 +24,10 @@ from geometry.VQT import vlen
 
 from model.elements import Singlet
 from utilities.Log import redmsg, orangemsg
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from commands.Fuse.FusePropertyManager import FusePropertyManager
-from icon_utilities import geticon
-from constants import diINVISIBLE
+from utilities.icon_utilities import geticon
+from utilities.constants import diINVISIBLE
 
 from commands.Move.Move_Command import Move_Command 
 from commands.Fuse.fusechunksMode import fusechunksBase
diff --git a/cad/src/commands/Fuse/FuseChunks_GraphicsMode.py b/cad/src/commands/Fuse/FuseChunks_GraphicsMode.py
index 5fe2252f7..2a9a51c33 100755
--- a/cad/src/commands/Fuse/FuseChunks_GraphicsMode.py
+++ b/cad/src/commands/Fuse/FuseChunks_GraphicsMode.py
@@ -15,10 +15,10 @@ Ninad 2008-01-25: Split Command and GraphicsMode classes
 from graphics.drawing.drawer import drawline
 from graphics.behaviors.shape import get_selCurve_color
 
-from constants import green
-from constants import magenta
-from constants import blue
-from constants import darkred
+from utilities.constants import green
+from utilities.constants import magenta
+from utilities.constants import blue
+from utilities.constants import darkred
 
 from commands.Move.Move_GraphicsMode import Move_GraphicsMode
 from commands.Translate.TranslateChunks_GraphicsMode import TranslateChunks_GraphicsMode
diff --git a/cad/src/commands/Fuse/fusechunksMode.py b/cad/src/commands/Fuse/fusechunksMode.py
index a0b6fc695..2b3cea8c2 100755
--- a/cad/src/commands/Fuse/fusechunksMode.py
+++ b/cad/src/commands/Fuse/fusechunksMode.py
@@ -20,16 +20,16 @@ from model.elements import Singlet
 from commands.Move.modifyMode import modifyMode
 from model.bonds import bond_at_singlets
 from utilities.Log import redmsg, orangemsg
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from commands.Fuse.FusePropertyManager import FusePropertyManager
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from graphics.behaviors.shape import get_selCurve_color
 
-from constants import green
-from constants import magenta
-from constants import blue
-from constants import darkred
-from constants import diINVISIBLE
+from utilities.constants import green
+from utilities.constants import magenta
+from utilities.constants import blue
+from utilities.constants import darkred
+from utilities.constants import diINVISIBLE
 
 MAKEBONDS = 'Make Bonds Between Chunks'
 FUSEATOMS = 'Fuse Overlapping Atoms'
diff --git a/cad/src/commands/GridPlaneProperties/GridPlaneProp.py b/cad/src/commands/GridPlaneProperties/GridPlaneProp.py
index 14809b0a0..0ea340856 100755
--- a/cad/src/commands/GridPlaneProperties/GridPlaneProp.py
+++ b/cad/src/commands/GridPlaneProperties/GridPlaneProp.py
@@ -62,7 +62,7 @@ class GridPlaneProp(QDialog, Ui_GridPlanePropDialog):
         
     def _set_xyspacing_enabled(self, grid_type):
         '''If <grid_type> == 1, which is SiC type, disable x, y spacing comboBox, otherwise, enable it. '''
-        from prefs_constants import SiC_GRID, SQUARE_GRID
+        from utilities.prefs_constants import SiC_GRID, SQUARE_GRID
         
         if grid_type == SiC_GRID:
             self.x_spacing_spinbox.setEnabled(False)
diff --git a/cad/src/commands/InsertGraphene/GrapheneGenerator.py b/cad/src/commands/InsertGraphene/GrapheneGenerator.py
index 2633f6877..9a963ccb9 100755
--- a/cad/src/commands/InsertGraphene/GrapheneGenerator.py
+++ b/cad/src/commands/InsertGraphene/GrapheneGenerator.py
@@ -23,7 +23,7 @@ import model.bond_constants as bond_constants
 
 from model.chunk import Chunk
 import foundation.env as env
-from debug import Stopwatch
+from utilities.debug import Stopwatch
 from model.elements import PeriodicTable
 from utilities.Log import greenmsg
 
diff --git a/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py b/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py
index c2a5d6b9f..163877602 100755
--- a/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py
+++ b/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py
@@ -24,14 +24,14 @@ reload(CoNTubGenerator)
 import os, sys, time
 
 import foundation.env as env
-import Initialize
+import utilities.Initialize as Initialize
 from utilities.Log import quote_html, redmsg ##, orangemsg, greenmsg
 from command_support.ParameterDialog import ParameterDialog, ParameterPane
 from command_support.GeneratorController import GeneratorController
 from command_support.GeneratorBaseClass import UserError, PluginBug ##, CadBug
-from debug import print_compact_traceback
-from PlatformDependent import find_or_make_any_directory, tempfiles_dir, find_plugin_dir
-import EndUser
+from utilities.debug import print_compact_traceback
+from platform.PlatformDependent import find_or_make_any_directory, tempfiles_dir, find_plugin_dir
+import utilities.EndUser as EndUser
 
 debug_install = False
 
@@ -43,7 +43,7 @@ def debug_run():
 ### one current bug: menu icon is nondeterministic. guess: need to keep a reference to the iconset that we make for it.
 # that seemed to help at first, but it's not enough, bug still happens sometimes when we reload this a lot! ####@@@@
 
-from debug_prefs import use_property_pane
+from utilities.debug_prefs import use_property_pane
 
 # ==
 
@@ -54,7 +54,7 @@ def add_insert_menu_item(win, command, name_of_what_to_insert, options = ()): ##
     undo_cmdname = "Insert %s" % (name_of_what_to_insert,) ## get this from caller, or, make it available to the command as it runs
         ###e but need to translate it ourselves, ##qApp.translate("Main Window", "Recent Files", None)
     ## self.connect(self.recentFilePopupMenu, SIGNAL('activated (int)'), self._openRecentFile)
-    from menu_helpers import insert_command_into_menu
+    from widgets.menu_helpers import insert_command_into_menu
     insert_command_into_menu( menu, menutext, command, options = options, position = menuIndex, undo_cmdname = undo_cmdname)
     return
 
@@ -327,7 +327,7 @@ class PluginlikeGenerator:
         return
 
     def imagename_to_pixmap(self, imagename): # KLUGE, see comment where dialog_env is set to self ###@@@ might work but untested ###@@@
-        from icon_utilities import imagename_to_pixmap
+        from utilities.icon_utilities import imagename_to_pixmap
         path = None
         for trydir in [self.plugin_dir, os.path.join(self.plugin_dir, "images")]:
             trypath = os.path.join( trydir, imagename )
diff --git a/cad/src/commands/InsertNanotube/NanotubeGenerator.py b/cad/src/commands/InsertNanotube/NanotubeGenerator.py
index e23ce309e..40816a145 100755
--- a/cad/src/commands/InsertNanotube/NanotubeGenerator.py
+++ b/cad/src/commands/InsertNanotube/NanotubeGenerator.py
@@ -16,7 +16,7 @@ from Numeric import dot
 from geometry.VQT import vlen, cross, norm, V
 import foundation.env as env
 from utilities import debug_flags
-from debug import Stopwatch
+from utilities.debug import Stopwatch
 
 from model.chem import Atom
 
diff --git a/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py b/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py
index 26728ad7c..8844147a0 100755
--- a/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py
+++ b/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py
@@ -20,7 +20,7 @@ from PM.PM_DoubleSpinBox import PM_DoubleSpinBox
 from PM.PM_SpinBox       import PM_SpinBox
 
 from model.bonds import CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 ntBondLengths = [CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH]
 
diff --git a/cad/src/commands/InsertPeptide/PeptideGenerator.py b/cad/src/commands/InsertPeptide/PeptideGenerator.py
index 339e27a11..e29492340 100755
--- a/cad/src/commands/InsertPeptide/PeptideGenerator.py
+++ b/cad/src/commands/InsertPeptide/PeptideGenerator.py
@@ -28,7 +28,7 @@ from model.bonds import bond_atoms
 from model.bonds import NeighborhoodGenerator
 from model.bond_constants import atoms_are_bonded
 from model.bond_constants import V_SINGLE, V_DOUBLE, V_AROMATIC
-from bonds_from_atoms import inferBonds
+from operations.bonds_from_atoms import inferBonds
 
 from Numeric import zeros, array, sqrt, pi, sin, cos, dot, Float
 from geometry.VQT import vlen, cross, norm, V
diff --git a/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py b/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py
index ec48faa6c..59f64394e 100755
--- a/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py
+++ b/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py
@@ -31,7 +31,7 @@ from PM.PM_PushButton     import PM_PushButton
 from PM.PM_ToolButtonGrid import PM_ToolButtonGrid
 from PM.PM_TextEdit       import PM_TextEdit
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from utilities.Log import orangemsg, greenmsg, redmsg
 import foundation.env as env
diff --git a/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py b/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py
index cdd6753f4..ad8c1106a 100644
--- a/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py
+++ b/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py
@@ -21,7 +21,7 @@ from widgets.widget_helpers import RGBf_to_QColor
 
 from command_support.MotorPropertyManager import MotorPropertyManager
 
-from constants import gray
+from utilities.constants import gray
 
 class LinearMotorPropertyManager(MotorPropertyManager):
     """
diff --git a/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py b/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py
index 1fc3a3e15..bff4102a2 100644
--- a/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py
+++ b/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py
@@ -13,7 +13,7 @@ ninad 2007-10-09: Created.
 import foundation.env as env
 from utilities.Log   import redmsg, greenmsg, orangemsg
 from model.jigs_motors import LinearMotor
-from jigmakers_Mixin import atom_limit_exceeded_and_confirmed
+from operations.jigmakers_Mixin import atom_limit_exceeded_and_confirmed
 from command_support.EditCommand import EditCommand
 
 from commands.SelectAtoms.SelectAtoms_GraphicsMode import SelectAtoms_GraphicsMode
diff --git a/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py b/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py
index d2d32f9a7..b5c4c1b0c 100755
--- a/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py
+++ b/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py
@@ -19,25 +19,25 @@ from PyQt4.Qt import QDoubleValidator
 
 from utilities.Log import greenmsg, redmsg, orangemsg, _graymsg, quote_html
 from commands.MinimizeEnergy.MinimizeEnergyPropDialog import Ui_MinimizeEnergyPropDialog
-from GroupButtonMixin import GroupButtonMixin
-from Sponsors import SponsorableMixin
-from icon_utilities import geticon
+from PM.GroupButtonMixin import GroupButtonMixin
+from sponsors.Sponsors import SponsorableMixin
+from utilities.icon_utilities import geticon
 
-from prefs_constants import Minimize_watchRealtimeMinimization_prefs_key
-from prefs_constants import Minimize_endRMS_prefs_key as endRMS_prefs_key
-from prefs_constants import Minimize_endMax_prefs_key as endMax_prefs_key
-from prefs_constants import Minimize_cutoverRMS_prefs_key as cutoverRMS_prefs_key
-from prefs_constants import Minimize_cutoverMax_prefs_key as cutoverMax_prefs_key
-from prefs_constants import Minimize_minimizationEngine_prefs_key
-from prefs_constants import electrostaticsForDnaDuringMinimize_prefs_key
+from utilities.prefs_constants import Minimize_watchRealtimeMinimization_prefs_key
+from utilities.prefs_constants import Minimize_endRMS_prefs_key as endRMS_prefs_key
+from utilities.prefs_constants import Minimize_endMax_prefs_key as endMax_prefs_key
+from utilities.prefs_constants import Minimize_cutoverRMS_prefs_key as cutoverRMS_prefs_key
+from utilities.prefs_constants import Minimize_cutoverMax_prefs_key as cutoverMax_prefs_key
+from utilities.prefs_constants import Minimize_minimizationEngine_prefs_key
+from utilities.prefs_constants import electrostaticsForDnaDuringMinimize_prefs_key
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 import foundation.env as env
 from utilities import debug_flags
 from ne1_ui.UserPrefs import get_pref_or_optval
 from widgets.widget_helpers import double_fixup
-from debug_prefs import debug_pref, Choice_boolean_False
-from prefs_widgets import connect_checkbox_with_boolean_pref
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
+from widgets.prefs_widgets import connect_checkbox_with_boolean_pref
 
 class MinimizeEnergyProp(QDialog, SponsorableMixin, GroupButtonMixin, Ui_MinimizeEnergyPropDialog):
 
@@ -139,7 +139,7 @@ class MinimizeEnergyProp(QDialog, SponsorableMixin, GroupButtonMixin, Ui_Minimiz
     def setup_ruc(self):
         "#doc"
         #bruce 060705 use new common code, if it works
-        from widget_controllers import realtime_update_controller
+        from widgets.widget_controllers import realtime_update_controller
         self.ruc = realtime_update_controller( 
             #( self.update_btngrp, self.update_number_spinbox, self.update_units_combobox ),
             ( self.update_btngrp_group, self.update_number_spinbox, self.update_units_combobox ),
@@ -208,9 +208,9 @@ class MinimizeEnergyProp(QDialog, SponsorableMixin, GroupButtonMixin, Ui_Minimiz
         # (should we pass these as arg to Minimize_CommandRun rather than thru env.prefs??)
         if debug_flags.atom_debug:
             print "debug: reloading runSim on each use, for development"
-            import runSim, debug
+            import simulation.runSim as runSim, utilities.debug as debug
             debug.reload_once_per_event(runSim)
-        from runSim import Minimize_CommandRun
+        from simulation.runSim import Minimize_CommandRun
         # do this in gather?
         if self.minimize_all_rbtn.isChecked():
             self.seltype = 'All'
diff --git a/cad/src/commands/Move/MovePropertyManager.py b/cad/src/commands/Move/MovePropertyManager.py
index e9e8f4958..9b8381190 100755
--- a/cad/src/commands/Move/MovePropertyManager.py
+++ b/cad/src/commands/Move/MovePropertyManager.py
@@ -601,7 +601,7 @@ class MovePropertyManager(Ui_MovePropertyManager):
             self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault  =  True )
             return
 
-        from ops_select import objectSelected
+        from operations.ops_select import objectSelected
         if objectSelected(self.o.assy):
             msg = ""
         else:
diff --git a/cad/src/commands/Move/Move_Command.py b/cad/src/commands/Move/Move_Command.py
index 8b302df9e..a640cbe54 100755
--- a/cad/src/commands/Move/Move_Command.py
+++ b/cad/src/commands/Move/Move_Command.py
@@ -27,13 +27,13 @@ import foundation.changes as changes
 from PyQt4 import QtGui
 from PyQt4.Qt import SIGNAL
 from commands.Move.MovePropertyManager import MovePropertyManager
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from commands.SelectChunks.SelectChunks_Command import SelectChunks_basicCommand
 from command_support.GraphicsMode_API import GraphicsMode_API
 from geometry.BoundingBox import BBox
 from utilities.Log import redmsg
 from geometry.VQT import V, Q
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from commands.Translate.TranslateChunks_GraphicsMode import TranslateChunks_GraphicsMode
 from commands.Rotate.RotateChunks_GraphicsMode import RotateChunks_GraphicsMode
 
diff --git a/cad/src/commands/Move/Move_GraphicsMode.py b/cad/src/commands/Move/Move_GraphicsMode.py
index 9fa7ad02b..d99be27a2 100755
--- a/cad/src/commands/Move/Move_GraphicsMode.py
+++ b/cad/src/commands/Move/Move_GraphicsMode.py
@@ -19,10 +19,10 @@ from PyQt4.Qt import Qt
 import foundation.env as env
 from geometry.VQT import V, Q, A, vlen, norm
 from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
-from constants import SUBTRACT_FROM_SELECTION
-from constants import ADD_TO_SELECTION
-from constants import START_NEW_SELECTION
-from constants import DELETE_SELECTION
+from utilities.constants import SUBTRACT_FROM_SELECTION
+from utilities.constants import ADD_TO_SELECTION
+from utilities.constants import START_NEW_SELECTION
+from utilities.constants import DELETE_SELECTION
 
 _superclass = SelectChunks_GraphicsMode
 
diff --git a/cad/src/commands/PartLibrary/PartLibraryMode.py b/cad/src/commands/PartLibrary/PartLibraryMode.py
index 2335ce09f..8ef2cdab1 100644
--- a/cad/src/commands/PartLibrary/PartLibraryMode.py
+++ b/cad/src/commands/PartLibrary/PartLibraryMode.py
@@ -30,7 +30,7 @@ from utilities.Log import orangemsg, greenmsg, quote_html, redmsg
 from model.chem import Atom
 from model.elements import Singlet
 from geometry.VQT import Q
-from ops_copy        import copied_nodes_for_DND
+from operations.ops_copy import copied_nodes_for_DND
 
 from commands.Paste.PasteMode import PasteMode
 from commands.PartLibrary.PartLibPropertyManager import PartLibPropertyManager
@@ -318,7 +318,7 @@ class PartLibraryMode(PasteMode):
                         #so we should turn this into history message,
                         # not a bug print. But I'm not positive it's possible
                         #w/o a bug, so review first. ###FIX [bruce 070501 comment]
-                    import debug
+                    import utilities.debug as debug
                     debug._bugnodes = nodes
                     newnodes = []
                 msg = redmsg( "error: nothing to deposit in [%s]" % quote_html(str(newPart.name)) )
@@ -340,7 +340,7 @@ class PartLibraryMode(PasteMode):
                     #saved only once by users (due to NE1 bug in save)
                     dirjunk, base = os.path.split(newPart.name)
                     basename, extjunk = os.path.splitext(base)
-                from constants import gensym
+                from utilities.constants import gensym
                 newnode.name = gensym( basename + " " ) # name library part 
                 #based on basename recorded in its mmp file's top node
                 newnode.move(moveOffset) #k not sure this method is correctly 
diff --git a/cad/src/commands/Paste/PasteMode.py b/cad/src/commands/Paste/PasteMode.py
index 4703cadd2..e22b2e596 100644
--- a/cad/src/commands/Paste/PasteMode.py
+++ b/cad/src/commands/Paste/PasteMode.py
@@ -28,10 +28,10 @@ from foundation.Group import Group
 from model.chem import Atom
 from model.chunk import Chunk
 from model.elements import Singlet
-from pastables     import is_pastable
+from operations.pastables import is_pastable
 from commands.BuildAtoms.depositMode import depositMode
 
-from pastables  import find_hotspot_for_pasting
+from operations.pastables import find_hotspot_for_pasting
 from model.bonds import bond_at_singlets
 
 from commands.Paste.PastePropertyManager import PastePropertyManager
diff --git a/cad/src/commands/PlayMovie/MoviePropertyManager.py b/cad/src/commands/PlayMovie/MoviePropertyManager.py
index 81795f2dc..fdbc30db8 100755
--- a/cad/src/commands/PlayMovie/MoviePropertyManager.py
+++ b/cad/src/commands/PlayMovie/MoviePropertyManager.py
@@ -16,7 +16,7 @@ from commands.PlayMovie.Ui_MoviePropertyManager import Ui_MoviePropertyManager
 from PyQt4.Qt import Qt, SIGNAL, QFileDialog, QString, QMessageBox
 import os, foundation.env as env
 from utilities.Log import redmsg, greenmsg
-from constants import filesplit
+from utilities.constants import filesplit
 
 class MoviePropertyManager(Ui_MoviePropertyManager):
     """
@@ -304,7 +304,7 @@ class MoviePropertyManager(Ui_MoviePropertyManager):
         # Check if file with name fn is a movie file which is valid for the current Part
         # [bruce 050324 made that a function and made it print the history messages
         #  which I've commented out below.]
-        from movie import _checkMovieFile
+        from simulation.movie import _checkMovieFile
         r = _checkMovieFile(self.w.assy.part, fn)
 
         if r == 1:
@@ -320,7 +320,7 @@ class MoviePropertyManager(Ui_MoviePropertyManager):
             return
 
         #bruce 050427 rewrote the following to use a new Movie object
-        from movie import find_saved_movie
+        from simulation.movie import find_saved_movie
         new_movie = find_saved_movie( self.w.assy, fn )
         if new_movie:
             new_movie.set_alist_from_entire_part(self.w.assy.part) # kluge? might need changing...
diff --git a/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py b/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py
index 9aa276e5d..abf81908c 100755
--- a/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py
+++ b/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py
@@ -33,8 +33,8 @@ from PM.PM_Constants     import pmDoneButton
 from PM.PM_Constants     import pmWhatsThisButton
 from PM.PM_Constants     import pmCancelButton
 
-from NE1ToolBar          import NE1ToolBar
-from icon_utilities      import geticon
+from widgets.NE1ToolBar import NE1ToolBar
+from utilities.icon_utilities import geticon
 
 class Ui_MoviePropertyManager(PM_Dialog):
     """
diff --git a/cad/src/commands/PlayMovie/movieMode.py b/cad/src/commands/PlayMovie/movieMode.py
index b0ccd6e82..167ec88e6 100755
--- a/cad/src/commands/PlayMovie/movieMode.py
+++ b/cad/src/commands/PlayMovie/movieMode.py
@@ -27,14 +27,14 @@ from PyQt4.Qt import QMessageBox, QString, QWidgetAction, QAction
 import foundation.env as env
 import foundation.changes as changes
 
-from movie import find_saved_movie
+from simulation.movie import find_saved_movie
 from command_support.modes import basicMode
 from utilities.Log import greenmsg
 from utilities.Log import redmsg, orangemsg
 from commands.PlayMovie.MoviePropertyManager import MoviePropertyManager
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
-from prefs_constants import workingDirectory_prefs_key
+from utilities.prefs_constants import workingDirectory_prefs_key
 
 class MovieRewindDialog(QDialog):
 
@@ -388,7 +388,7 @@ def simMoviePlayer(assy):
     either the current movie if any, or a previously saved
     dpb file with the same name as the current part, if one can be found.
     """
-    from movie import find_saved_movie, Movie #bruce 050329 precaution (in case of similar bug to bug 499)
+    from simulation.movie import find_saved_movie, Movie #bruce 050329 precaution (in case of similar bug to bug 499)
     win = assy.w
     if not assy.molecules: # No model, so no movie could be valid for current part.
         # bruce 050327 comment: even so, a movie file might be valid for some other Part...
diff --git a/cad/src/commands/Plot/PlotTool.py b/cad/src/commands/Plot/PlotTool.py
index a921af5f8..749a56b44 100755
--- a/cad/src/commands/Plot/PlotTool.py
+++ b/cad/src/commands/Plot/PlotTool.py
@@ -19,10 +19,10 @@ from PyQt4.Qt import QStringList
 
 from commands.Plot.PlotToolDialog import Ui_PlotToolDialog
 from utilities.Log import redmsg, greenmsg, orangemsg
-from movie import find_saved_movie
-from PlatformDependent import open_file_in_editor
+from simulation.movie import find_saved_movie
+from platform.PlatformDependent import open_file_in_editor
 import foundation.env as env
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 debug_gnuplot = False
 
@@ -289,7 +289,7 @@ class PlotTool(QWidget, Ui_PlotToolDialog):
                 
         plotProcess = None
         try:
-            from Process import Process
+            from processes.Process import Process
             plotProcess = Process()
             
             # Run gnuplot as a new, separate process. 
diff --git a/cad/src/commands/PovraySceneProperties/PovraySceneProp.py b/cad/src/commands/PovraySceneProperties/PovraySceneProp.py
index 0c16cc375..194faab46 100755
--- a/cad/src/commands/PovraySceneProperties/PovraySceneProp.py
+++ b/cad/src/commands/PovraySceneProperties/PovraySceneProp.py
@@ -14,8 +14,8 @@ from PyQt4.Qt import SIGNAL, QDialog, QWhatsThis, QDialog
 from commands.PovraySceneProperties.PovrayScenePropDialog import Ui_PovrayScenePropDialog
 import foundation.env as env, os
 from utilities.Log import redmsg, greenmsg
-from GroupButtonMixin import GroupButtonMixin
-from Sponsors import SponsorableMixin
+from PM.GroupButtonMixin import GroupButtonMixin
+from sponsors.Sponsors import SponsorableMixin
 from utilities.Comparison import same_vals
 
 class PovraySceneProp(QDialog, SponsorableMixin, GroupButtonMixin, Ui_PovrayScenePropDialog):
diff --git a/cad/src/commands/PovraySceneProperties/PovrayScenePropDialog.py b/cad/src/commands/PovraySceneProperties/PovrayScenePropDialog.py
index 3b9175d3a..a1226bf23 100755
--- a/cad/src/commands/PovraySceneProperties/PovrayScenePropDialog.py
+++ b/cad/src/commands/PovraySceneProperties/PovrayScenePropDialog.py
@@ -9,9 +9,9 @@
 # WARNING! All changes made in this file will be lost!
 
 from PyQt4 import QtCore, QtGui
-from icon_utilities import geticon
-from PropMgr_Constants import getHeaderFont
-from PropMgr_Constants import pmLabelLeftAlignment
+from utilities.icon_utilities import geticon
+from PM.PropMgr_Constants import getHeaderFont
+from PM.PropMgr_Constants import pmLabelLeftAlignment
 
 class Ui_PovrayScenePropDialog(object):
     def setupUi(self, PovrayScenePropDialog):
diff --git a/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py b/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py
index aa7581ebf..8d3838af2 100755
--- a/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py
+++ b/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py
@@ -23,7 +23,7 @@ from PM.PM_CheckBox      import PM_CheckBox
 from PM.PM_PushButton    import PM_PushButton
 
 from widgets.widget_helpers import RGBf_to_QColor
-from constants import gray
+from utilities.constants import gray
 
 from command_support.MotorPropertyManager import MotorPropertyManager
 
diff --git a/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py b/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py
index 7461d6ec3..317300296 100644
--- a/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py
+++ b/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py
@@ -13,7 +13,7 @@ ninad 2007-10-09: Created. This deprecates 'RotoryMotorGenerator'
 import foundation.env as env
 from utilities.Log   import redmsg, greenmsg, orangemsg
 from model.jigs_motors import RotaryMotor
-from jigmakers_Mixin import atom_limit_exceeded_and_confirmed
+from operations.jigmakers_Mixin import atom_limit_exceeded_and_confirmed
 from command_support.EditCommand import EditCommand
 
 from commands.SelectAtoms.SelectAtoms_GraphicsMode import SelectAtoms_GraphicsMode
diff --git a/cad/src/commands/Rotate/RotateChunks_GraphicsMode.py b/cad/src/commands/Rotate/RotateChunks_GraphicsMode.py
index be854c018..5f0d9e0ff 100755
--- a/cad/src/commands/Rotate/RotateChunks_GraphicsMode.py
+++ b/cad/src/commands/Rotate/RotateChunks_GraphicsMode.py
@@ -22,7 +22,7 @@ from Numeric import dot, sign
 import foundation.env as env
 from utilities.Log import redmsg
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from geometry.VQT import V, Q, A, vlen, norm
 from commands.Move.Move_GraphicsMode import Move_GraphicsMode
 
diff --git a/cad/src/commands/Select/Select_GraphicsMode.py b/cad/src/commands/Select/Select_GraphicsMode.py
index 9895d7f68..1895dbf42 100755
--- a/cad/src/commands/Select/Select_GraphicsMode.py
+++ b/cad/src/commands/Select/Select_GraphicsMode.py
@@ -79,19 +79,19 @@ from OpenGL.GL import glSelectBuffer
 from OpenGL.GLU import gluProject
 from OpenGL.GLU import gluUnProject
 
-from constants import GL_FAR_Z
-from constants import SELSHAPE_RECT
-from constants import SELSHAPE_LASSO
-from constants import SUBTRACT_FROM_SELECTION
-from constants import ADD_TO_SELECTION
-from constants import START_NEW_SELECTION
-from constants import DELETE_SELECTION
+from utilities.constants import GL_FAR_Z
+from utilities.constants import SELSHAPE_RECT
+from utilities.constants import SELSHAPE_LASSO
+from utilities.constants import SUBTRACT_FROM_SELECTION
+from utilities.constants import ADD_TO_SELECTION
+from utilities.constants import START_NEW_SELECTION
+from utilities.constants import DELETE_SELECTION
 
-from constants import black
+from utilities.constants import black
 
 import foundation.env as env
-from debug_prefs import debug_pref
-from debug_prefs import Choice
+from utilities.debug_prefs import debug_pref
+from utilities.debug_prefs import Choice
 
 from geometry.VQT import V, A, vlen
 
@@ -100,11 +100,11 @@ from model.bonds import Bond
 from model.chem import Atom 
 from model.jigs import Jig
 
-from debug import print_compact_traceback
-from debug import print_compact_stack
+from utilities.debug import print_compact_traceback
+from utilities.debug import print_compact_stack
 
-from prefs_constants import bondHighlightColor_prefs_key
-from prefs_constants import deleteBondHighlightColor_prefs_key
+from utilities.prefs_constants import bondHighlightColor_prefs_key
+from utilities.prefs_constants import deleteBondHighlightColor_prefs_key
 
 from utilities import debug_flags
 
diff --git a/cad/src/commands/Select/Select_GraphicsMode_DrawMethod_preMixin.py b/cad/src/commands/Select/Select_GraphicsMode_DrawMethod_preMixin.py
index cf3571563..8afae3f52 100755
--- a/cad/src/commands/Select/Select_GraphicsMode_DrawMethod_preMixin.py
+++ b/cad/src/commands/Select/Select_GraphicsMode_DrawMethod_preMixin.py
@@ -26,9 +26,9 @@ from OpenGL.GL import glTranslate
 
 from utilities.Log import redmsg
 
-from debug_prefs import debug_pref
-from debug_prefs import Choice
-from debug import print_compact_stack
+from utilities.debug_prefs import debug_pref
+from utilities.debug_prefs import Choice
+from utilities.debug import print_compact_stack
 
 from command_support.GraphicsMode import commonGraphicsMode
 
diff --git a/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py b/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py
index 74873008c..0330b85df 100755
--- a/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py
+++ b/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py
@@ -23,10 +23,10 @@ import foundation.env as env
 from model.bonds import Bond
 from model.chem import Atom 
 from model.jigs import Jig
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 debug_update_selobj_calls = False # do not commit with true
 
-from GlobalPreferences import DEBUG_BAREMOTION, DEBUG_BAREMOTION_VERBOSE
+from utilities.GlobalPreferences import DEBUG_BAREMOTION, DEBUG_BAREMOTION_VERBOSE
 
 _count = 0
 
diff --git a/cad/src/commands/Select/selectMode.py b/cad/src/commands/Select/selectMode.py
index 71d1e08d8..74a1de724 100755
--- a/cad/src/commands/Select/selectMode.py
+++ b/cad/src/commands/Select/selectMode.py
@@ -32,7 +32,7 @@ from commands.Select.Select_GraphicsMode import Select_basicGraphicsMode
 
 from command_support.modes import anyMode
 
-from constants import GLPANE_IS_COMMAND_SEQUENCER
+from utilities.constants import GLPANE_IS_COMMAND_SEQUENCER
 
 class selectMode(Select_basicCommand, 
                  Select_basicGraphicsMode,
diff --git a/cad/src/commands/SelectAtoms/SelectAtoms_Command.py b/cad/src/commands/SelectAtoms/SelectAtoms_Command.py
index 9050e7ff4..72826c8fb 100755
--- a/cad/src/commands/SelectAtoms/SelectAtoms_Command.py
+++ b/cad/src/commands/SelectAtoms/SelectAtoms_Command.py
@@ -29,8 +29,8 @@ Ninad & Bruce 2007-12-13: Created new Command and GraphicsMode classes from
 
 """
 from utilities import debug_flags
-from runSim import LocalMinimize_function
-from debug import print_compact_traceback
+from simulation.runSim import LocalMinimize_function
+from utilities.debug import print_compact_traceback
 
 from commands.Select.Select_Command import Select_basicCommand
 from command_support.GraphicsMode_API import GraphicsMode_API
@@ -140,7 +140,7 @@ class SelectAtoms_basicCommand(Select_basicCommand):
         if debug_flags.atom_debug:
             print "debug: reloading runSim on each use, for development"\
                   "[localmin %s, %d]" % (atom, nlayers)
-            import runSim, debug
+            import simulation.runSim as runSim, utilities.debug as debug
             debug.reload_once_per_event(runSim) #bruce 060705 revised this
         if 1:
             # this does not work, 
diff --git a/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py b/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py
index b0752c11e..43c82dc71 100755
--- a/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py
+++ b/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py
@@ -40,21 +40,21 @@ from model.jigs import Jig
 from model.bonds import Bond
 from model.elements import Singlet
 
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 
 from foundation.Group import Group
 
 from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT
 
-from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
 
-from prefs_constants import bondHighlightColor_prefs_key
-from prefs_constants import bondpointHighlightColor_prefs_key
-from prefs_constants import atomHighlightColor_prefs_key
-from prefs_constants import deleteBondHighlightColor_prefs_key
-from prefs_constants import deleteAtomHighlightColor_prefs_key
+from utilities.prefs_constants import bondHighlightColor_prefs_key
+from utilities.prefs_constants import bondpointHighlightColor_prefs_key
+from utilities.prefs_constants import atomHighlightColor_prefs_key
+from utilities.prefs_constants import deleteBondHighlightColor_prefs_key
+from utilities.prefs_constants import deleteAtomHighlightColor_prefs_key
 
-from constants import average_value
+from utilities.constants import average_value
 
 from utilities.Log import orangemsg
 
diff --git a/cad/src/commands/SelectAtoms/selectAtomsMode.py b/cad/src/commands/SelectAtoms/selectAtomsMode.py
index 11bf6153b..a83792ffb 100755
--- a/cad/src/commands/SelectAtoms/selectAtomsMode.py
+++ b/cad/src/commands/SelectAtoms/selectAtomsMode.py
@@ -31,8 +31,8 @@ Ninad & Bruce 2007-12-13: Created new Command and GraphicsMode classes from
 
 """
 
-from debug import print_compact_traceback
-from constants import GLPANE_IS_COMMAND_SEQUENCER
+from utilities.debug import print_compact_traceback
+from utilities.constants import GLPANE_IS_COMMAND_SEQUENCER
 
 from commands.SelectAtoms.SelectAtoms_Command import SelectAtoms_basicCommand
 from commands.SelectAtoms.SelectAtoms_GraphicsMode import SelectAtoms_basicGraphicsMode
diff --git a/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py b/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py
index 75db04953..d348bc232 100755
--- a/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py
+++ b/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py
@@ -39,11 +39,11 @@ from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT
 from model.chunk import Chunk
 from graphics.drawing.drawer import apply_material, allow_color_sorting, use_color_sorted_dls
 from OpenGL.GL import glCallList
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 
-from constants import yellow, orange, ave_colors, red
+from utilities.constants import yellow, orange, ave_colors, red
 
-from debug_prefs import debug_pref, Choice_boolean_True
+from utilities.debug_prefs import debug_pref, Choice_boolean_True
 from utilities import debug_flags
 
 from geometry.VQT import V, vlen
@@ -52,7 +52,7 @@ import time
 
 from commands.Select.Select_GraphicsMode import Select_basicGraphicsMode
 
-from GlobalPreferences import DEBUG_BAREMOTION
+from utilities.GlobalPreferences import DEBUG_BAREMOTION
 
 _superclass = Select_basicGraphicsMode
 
diff --git a/cad/src/commands/SelectChunks/selectMolsMode.py b/cad/src/commands/SelectChunks/selectMolsMode.py
index 8c6bdbb54..996f8804c 100755
--- a/cad/src/commands/SelectChunks/selectMolsMode.py
+++ b/cad/src/commands/SelectChunks/selectMolsMode.py
@@ -16,7 +16,7 @@ Ninad & Bruce 2007-12-13: Created new Command and GraphicsMode classes from
                           SelectChunks_GraphicsMode.py]
 """
 
-from constants import GLPANE_IS_COMMAND_SEQUENCER
+from utilities.constants import GLPANE_IS_COMMAND_SEQUENCER
 
 from commands.SelectChunks.SelectChunks_Command import SelectChunks_basicCommand
 from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_basicGraphicsMode
diff --git a/cad/src/commands/Translate/TranslateChunks_GraphicsMode.py b/cad/src/commands/Translate/TranslateChunks_GraphicsMode.py
index 20dc8a592..5d4bc1b16 100755
--- a/cad/src/commands/Translate/TranslateChunks_GraphicsMode.py
+++ b/cad/src/commands/Translate/TranslateChunks_GraphicsMode.py
@@ -18,7 +18,7 @@ from utilities import debug_flags
 import math
 from Numeric import dot
 import foundation.env as env
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from geometry.VQT import V, A, vlen, norm
 from commands.Move.Move_GraphicsMode import Move_GraphicsMode
 
diff --git a/cad/src/dna/DnaSequenceEditor/DnaSequenceEditor.py b/cad/src/dna/DnaSequenceEditor/DnaSequenceEditor.py
index 48dc8b088..f4af48cbf 100644
--- a/cad/src/dna/DnaSequenceEditor/DnaSequenceEditor.py
+++ b/cad/src/dna/DnaSequenceEditor/DnaSequenceEditor.py
@@ -53,12 +53,12 @@ from dna.model.Dna_Constants import getReverseSequence
 
 from PM.PM_Colors import pmMessageBoxColor
 
-from prefs_constants import workingDirectory_prefs_key
+from utilities.prefs_constants import workingDirectory_prefs_key
 
 from dna.DnaSequenceEditor.Ui_DnaSequenceEditor import Ui_DnaSequenceEditor
 
 from utilities import debug_flags
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 class DnaSequenceEditor(Ui_DnaSequenceEditor):
     """
diff --git a/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py b/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py
index e0fa04697..00d0294eb 100644
--- a/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py
+++ b/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py
@@ -30,7 +30,7 @@ from PM.PM_TextEdit   import PM_TextEdit
 from PM.PM_LineEdit   import PM_LineEdit
 from PM.PM_PushButton import PM_PushButton
 
-from icon_utilities import geticon, getpixmap
+from utilities.icon_utilities import geticon, getpixmap
 
 class Ui_DnaSequenceEditor(PM_DockWidget):
     """
diff --git a/cad/src/dna/commands/BreakStrands/BreakStrands_Command.py b/cad/src/dna/commands/BreakStrands/BreakStrands_Command.py
index 716ad64c5..bab63173d 100644
--- a/cad/src/dna/commands/BreakStrands/BreakStrands_Command.py
+++ b/cad/src/dna/commands/BreakStrands/BreakStrands_Command.py
@@ -14,10 +14,10 @@ TODOs: [ as of 2008-01-04]
 import foundation.changes as changes
 from commands.BuildAtoms.BuildAtoms_GraphicsMode import BuildAtoms_GraphicsMode
 from commands.BuildAtoms.BuildAtoms_Command import BuildAtoms_Command
-from constants             import red
+from utilities.constants import red
 from dna.commands.BreakStrands.BreakStrands_PropertyManager import BreakStrands_PropertyManager
 
-from TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
+from temporary_commands.TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
 # == GraphicsMode part
 
 _superclass_for_GM = BuildAtoms_GraphicsMode
diff --git a/cad/src/dna/commands/BreakStrands/BreakStrands_PropertyManager.py b/cad/src/dna/commands/BreakStrands/BreakStrands_PropertyManager.py
index d12b7b6bc..e4552a300 100644
--- a/cad/src/dna/commands/BreakStrands/BreakStrands_PropertyManager.py
+++ b/cad/src/dna/commands/BreakStrands/BreakStrands_PropertyManager.py
@@ -18,7 +18,7 @@ button code (confirmation_corner)
 pending because of some remaining things in GBC cleanup (such as 
 NanotubeGenerator etc) 
 """
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from PM.PM_Dialog import PM_Dialog
 from PM.PM_Constants     import pmDoneButton
 from PM.PM_Constants     import pmWhatsThisButton
diff --git a/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py b/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py
index 65c80b677..4e4cee6dc 100644
--- a/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py
+++ b/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py
@@ -26,7 +26,7 @@ from dna.model.DnaGroup import DnaGroup
 from utilities.Log  import greenmsg
 from command_support.GeneratorBaseClass import PluginBug, UserError
 
-from constants import gensym
+from utilities.constants import gensym
 
 from ne1_ui.toolbars.Ui_DnaFlyout import DnaFlyout
 
diff --git a/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py b/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py
index 81244a906..ecf3ebddc 100644
--- a/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py
+++ b/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py
@@ -22,7 +22,7 @@ BUGS:
 - Just entering and leaving BuilddDna_EditCommand creates an empty DnaGroup
 """
 from utilities import debug_flags
-from debug import  print_compact_stack
+from utilities.debug import print_compact_stack
 
 from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QString
@@ -31,7 +31,7 @@ from PM.PM_GroupBox      import PM_GroupBox
 from PM.PM_PushButton    import PM_PushButton
 from PM.PM_SelectionListWidget import PM_SelectionListWidget
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 
 from PM.PM_Constants     import pmDoneButton
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplex.py b/cad/src/dna/commands/BuildDuplex/DnaDuplex.py
index f31f04ae7..3cfc02844 100644
--- a/cad/src/dna/commands/BuildDuplex/DnaDuplex.py
+++ b/cad/src/dna/commands/BuildDuplex/DnaDuplex.py
@@ -18,21 +18,21 @@ import random
 
 from math    import sin, cos, pi
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from PlatformDependent  import find_plugin_dir
+from platform.PlatformDependent import find_plugin_dir
 from files.mmp.files_mmp import readmmp
 from geometry.VQT import Q, V, angleBetween, cross, vlen
 from commands.Fuse.fusechunksMode import fusechunksBase
 from utilities.Log      import orangemsg
 from command_support.GeneratorBaseClass import PluginBug
-from constants          import gensym, darkred, blue, orange, olive
-from constants          import diBALL, diTUBES
-from prefs_constants import dnaDefaultSegmentColor_prefs_key
+from utilities.constants import gensym, darkred, blue, orange, olive
+from utilities.constants import diBALL, diTUBES
+from utilities.prefs_constants import dnaDefaultSegmentColor_prefs_key
 
 from dna.model.Dna_Constants import getDuplexBasesPerTurn
 
-from runSim import adjustSinglet
+from simulation.runSim import adjustSinglet
 
 from model.elements import PeriodicTable
 Element_Ae3 = PeriodicTable.getElement('Ae3')
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py b/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py
index 8901d9a01..d6a2db305 100644
--- a/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py
+++ b/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py
@@ -35,7 +35,7 @@ from PM.PM_ToolButton    import PM_ToolButton
 from PM.PM_CoordinateSpinBoxes import PM_CoordinateSpinBoxes
 from PM.PM_CheckBox   import PM_CheckBox
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 from geometry.VQT import V
 
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py b/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py
index 8e8c432af..8f779d520 100644
--- a/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py
+++ b/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py
@@ -35,7 +35,7 @@ from command_support.EditCommand import EditCommand
 
 from dna.model.DnaSegment import DnaSegment
 from dna.model.DnaGroup import DnaGroup
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 from utilities.Log  import redmsg, greenmsg
 from geometry.VQT import V, Veq, vlen
@@ -45,7 +45,7 @@ from dna.commands.BuildDuplex.DnaDuplex import B_Dna_PAM5
 from command_support.GeneratorBaseClass import PluginBug, UserError
 from dna.commands.BuildDuplex.DnaDuplexPropertyManager import DnaDuplexPropertyManager
 
-from constants import gensym
+from utilities.constants import gensym
 
 
 from dna.model.Dna_Constants import getNumberOfBasePairsFromDuplexLength
diff --git a/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py b/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py
index 97e2de8eb..e03bbb351 100755
--- a/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py
+++ b/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py
@@ -45,9 +45,9 @@ import re
 
 from math    import sin, cos, pi
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from PlatformDependent  import find_plugin_dir
+from platform.PlatformDependent import find_plugin_dir
 from files.mmp.files_mmp import readmmp
 from geometry.VQT import V
 from commands.Fuse.fusechunksMode import fusechunksBase
diff --git a/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py b/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py
index 0646415d3..e4f09de5e 100755
--- a/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py
+++ b/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py
@@ -29,14 +29,14 @@ Mark 2007-10-18:
 import foundation.env as env
 import random
 
-from constants import darkred, blue, lightgray
+from utilities.constants import darkred, blue, lightgray
 
 from foundation.Group import Group
 from utilities.Log  import redmsg, greenmsg ##, orangemsg
 from geometry.VQT import Q, V, angleBetween, cross, vlen, Veq
 from math           import pi
 from model.chunk import Chunk
-from constants      import gensym    
+from utilities.constants import gensym    
 
 from dna.model.Dna_Constants import basesDict, getReverseSequence
 from dna.commands.BuildDuplex_old.DnaGenHelper import B_Dna_PAM3, B_Dna_PAM5
diff --git a/cad/src/dna/commands/BuildDuplex_old/DnaGeneratorPropertyManager.py b/cad/src/dna/commands/BuildDuplex_old/DnaGeneratorPropertyManager.py
index d6498a042..25f3b4b3b 100755
--- a/cad/src/dna/commands/BuildDuplex_old/DnaGeneratorPropertyManager.py
+++ b/cad/src/dna/commands/BuildDuplex_old/DnaGeneratorPropertyManager.py
@@ -66,7 +66,7 @@ from PM.PM_SpinBox       import PM_SpinBox
 from PM.PM_TextEdit      import PM_TextEdit
 
 from PM.PM_Dialog import PM_Dialog
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 
 # DNA model type variables
 #  (indices for model... and conformation... comboboxes).
diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
index a0b1f3e63..8785281a5 100644
--- a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
+++ b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
@@ -52,18 +52,18 @@ from dna.commands.BuildDuplex.DnaDuplex import B_Dna_PAM5
 from command_support.GeneratorBaseClass import PluginBug, UserError
 
 
-from constants import gensym
+from utilities.constants import gensym
 
 from dna.model.Dna_Constants import getDuplexLength
-from test_connectWithState import State_preMixin
+from prototype.test_connectWithState import State_preMixin
 
-from constants import noop
+from utilities.constants import noop
 from exprs.attr_decl_macros import Instance, State
 
 from exprs.__Symbols__ import _self
 from exprs.Exprs import call_Expr
 from exprs.Exprs import norm_Expr
-from prefs_widgets import ObjAttr_StateRef
+from widgets.prefs_widgets import ObjAttr_StateRef
 from exprs.ExprsConstants import Width, Point
 
 from model.chunk import Chunk
diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py b/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py
index 7c57e174e..eb7d407b8 100644
--- a/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py
+++ b/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py
@@ -39,17 +39,17 @@ from dna.commands.BuildDna.BuildDna_GraphicsMode import BuildDna_GraphicsMode
 from dna.model.DnaSegment import DnaSegment
 
 from dna.temporary_commands.DnaLineMode import DnaLine_GM
-from TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
+from temporary_commands.TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
 
 from graphics.drawing.drawDnaRibbons import drawDnaRibbons
 
 import foundation.env as env
-from prefs_constants import bdnaBasesPerTurn_prefs_key
+from utilities.prefs_constants import bdnaBasesPerTurn_prefs_key
 
 import math
 from geometry.VQT import V, norm, A, Q, vlen
-from constants import darkred, blue, black
-from debug import print_compact_traceback
+from utilities.constants import darkred, blue, black
+from utilities.debug import print_compact_traceback
 
 from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT
 
diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py b/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py
index 7a8704fb3..1968c877d 100644
--- a/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py
+++ b/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py
@@ -10,7 +10,7 @@ See DnaSegment_EditCommand for details.
 from PyQt4.Qt import SIGNAL
 from PM.PM_GroupBox      import PM_GroupBox
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 
 from PM.PM_Constants     import pmDoneButton
diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_ResizeHandle.py b/cad/src/dna/commands/DnaSegment/DnaSegment_ResizeHandle.py
index 83af42e59..48519e3e2 100644
--- a/cad/src/dna/commands/DnaSegment/DnaSegment_ResizeHandle.py
+++ b/cad/src/dna/commands/DnaSegment/DnaSegment_ResizeHandle.py
@@ -24,8 +24,8 @@ from exprs.Rect             import Sphere
 
 from exprs.Arrow import Arrow
    
-from constants  import yellow, darkgreen
-from constants  import olive
+from utilities.constants import yellow, darkgreen
+from utilities.constants import olive
 
 from geometry.VQT import V
 from exprs.DraggableHandle import DraggableHandle_AlongLine
diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
index 83413d9ba..1847ab262 100644
--- a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
+++ b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
@@ -17,18 +17,18 @@ TODO: as of 2008-02-14
     methods in class dna_model.DnaSegment change. 
 
 """
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 from geometry.VQT import  V
 from geometry.VQT import  vlen
 from geometry.VQT import  norm
 
-from test_connectWithState import State_preMixin
+from prototype.test_connectWithState import State_preMixin
 from exprs.attr_decl_macros import Instance, State
 from exprs.__Symbols__ import _self
 from exprs.Exprs import call_Expr
 from exprs.Exprs import norm_Expr
-from prefs_widgets import ObjAttr_StateRef
+from widgets.prefs_widgets import ObjAttr_StateRef
 from exprs.ExprsConstants import Width, Point
 
 from model.chunk import Chunk
@@ -40,7 +40,7 @@ from dna.commands.DnaStrand.DnaStrand_ResizeHandle import DnaStrand_ResizeHandle
 
 from command_support.EditCommand import EditCommand 
 
-from constants import noop
+from utilities.constants import noop
 
 CYLINDER_WIDTH_DEFAULT_VALUE = 0.0
 
diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_GraphicsMode.py b/cad/src/dna/commands/DnaStrand/DnaStrand_GraphicsMode.py
index a5e194bd3..dcbe04cb8 100644
--- a/cad/src/dna/commands/DnaStrand/DnaStrand_GraphicsMode.py
+++ b/cad/src/dna/commands/DnaStrand/DnaStrand_GraphicsMode.py
@@ -11,7 +11,7 @@ Created 2008-02-14
 
 """
 from dna.commands.BuildDna.BuildDna_GraphicsMode import BuildDna_GraphicsMode
-from TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
+from temporary_commands.TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
 
 _superclass = BuildDna_GraphicsMode
 
diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py b/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py
index f842ae571..dacea17d9 100644
--- a/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py
+++ b/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py
@@ -12,12 +12,12 @@ its a child of that PM) . See if that creates any issues.
 - Copies some methods from BuildDna_PropertyManager. 
 """
 from utilities import debug_flags
-from debug import  print_compact_stack
+from utilities.debug import print_compact_stack
 
 from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QString
 
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from command_support.EditCommand_PM import EditCommand_PM
 
 from PM.PM_Constants     import pmDoneButton
diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_ResizeHandle.py b/cad/src/dna/commands/DnaStrand/DnaStrand_ResizeHandle.py
index e9fa7b33a..462a558cb 100644
--- a/cad/src/dna/commands/DnaStrand/DnaStrand_ResizeHandle.py
+++ b/cad/src/dna/commands/DnaStrand/DnaStrand_ResizeHandle.py
@@ -32,7 +32,7 @@ from exprs.ExprsConstants   import ORIGIN, DX
 from exprs.dna_ribbon_view  import Cylinder
 from exprs.Rect             import Sphere
    
-from constants              import  yellow, purple, darkgreen
+from utilities.constants import yellow, purple, darkgreen
 
 from geometry.VQT import V
 from exprs.DraggableHandle import DraggableHandle_AlongLine
diff --git a/cad/src/dna/commands/JoinStrands/JoinStrands_Command.py b/cad/src/dna/commands/JoinStrands/JoinStrands_Command.py
index 7d1f0be4c..0ce3c84e1 100644
--- a/cad/src/dna/commands/JoinStrands/JoinStrands_Command.py
+++ b/cad/src/dna/commands/JoinStrands/JoinStrands_Command.py
@@ -13,7 +13,7 @@ import foundation.changes as changes
 from commands.BuildAtoms.BuildAtoms_GraphicsMode import BuildAtoms_GraphicsMode
 from commands.BuildAtoms.BuildAtoms_Command import BuildAtoms_Command
 from dna.commands.JoinStrands.JoinStrands_PropertyManager import JoinStrands_PropertyManager
-from TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
+from temporary_commands.TemporaryCommand import ESC_to_exit_GraphicsMode_preMixin
 # == GraphicsMode part
 
 _superclass_for_GM = BuildAtoms_GraphicsMode
diff --git a/cad/src/dna/commands/JoinStrands/JoinStrands_PropertyManager.py b/cad/src/dna/commands/JoinStrands/JoinStrands_PropertyManager.py
index 69ca36604..3d8e115c4 100644
--- a/cad/src/dna/commands/JoinStrands/JoinStrands_PropertyManager.py
+++ b/cad/src/dna/commands/JoinStrands/JoinStrands_PropertyManager.py
@@ -19,7 +19,7 @@ pending because of some remaining things in GBC cleanup (such as
 NanotubeGenerator etc) 
 """
 import sys
-from DebugMenuMixin import DebugMenuMixin
+from widgets.DebugMenuMixin import DebugMenuMixin
 from PM.PM_Dialog import PM_Dialog
 from PM.PM_Constants     import pmDoneButton
 from PM.PM_Constants     import pmWhatsThisButton
diff --git a/cad/src/dna/model/Block.py b/cad/src/dna/model/Block.py
index 1a06b9c46..e43d1d5ad 100644
--- a/cad/src/dna/model/Block.py
+++ b/cad/src/dna/model/Block.py
@@ -12,7 +12,7 @@ might be moved into a more general package.
 
 from foundation.Group import Group
 
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 class Block(Group):
     """
diff --git a/cad/src/dna/model/DnaGroup.py b/cad/src/dna/model/DnaGroup.py
index efca57d2c..9cc9c0d9b 100644
--- a/cad/src/dna/model/DnaGroup.py
+++ b/cad/src/dna/model/DnaGroup.py
@@ -10,9 +10,9 @@ DnaGroup.py - ...
 from dna.model.Block import Block
 from model.chunk import Chunk
 
-from constants import gensym
+from utilities.constants import gensym
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 from dna.updater.dna_updater_globals import _f_DnaGroup_for_homeless_objects_in_Part
 
diff --git a/cad/src/dna/model/DnaLadderRailChunk.py b/cad/src/dna/model/DnaLadderRailChunk.py
index 0d151197a..d6ee8cb6f 100644
--- a/cad/src/dna/model/DnaLadderRailChunk.py
+++ b/cad/src/dna/model/DnaLadderRailChunk.py
@@ -12,10 +12,10 @@ from model.chunk import Chunk
 from model.elements import Singlet
 from model.elements import Pl5
 
-from constants import gensym
-from constants import black
-from constants import ave_colors
-from constants import diDEFAULT
+from utilities.constants import gensym
+from utilities.constants import black
+from utilities.constants import ave_colors
+from utilities.constants import diDEFAULT
 
 from utilities import debug_flags
 
@@ -27,7 +27,7 @@ from utilities.Log import orangemsg, graymsg
 
 from PyQt4.Qt import QFont, QString # for debug code
 
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 # see also:
 ## from dna_model.DnaLadder import _rail_end_atom_to_ladder
diff --git a/cad/src/dna/model/DnaMarker.py b/cad/src/dna/model/DnaMarker.py
index e83ccba0d..f0f114e4c 100644
--- a/cad/src/dna/model/DnaMarker.py
+++ b/cad/src/dna/model/DnaMarker.py
@@ -29,7 +29,7 @@ from utilities import debug_flags
 
 from graphics.drawing.drawer import drawwirecube
 
-from constants import orange
+from utilities.constants import orange
 
 from files.mmp.files_mmp_registration import MMP_RecordParser
 from files.mmp.files_mmp_registration import register_MMP_RecordParser
diff --git a/cad/src/dna/model/DnaSegment.py b/cad/src/dna/model/DnaSegment.py
index d5784b650..393338ca2 100644
--- a/cad/src/dna/model/DnaSegment.py
+++ b/cad/src/dna/model/DnaSegment.py
@@ -19,14 +19,14 @@ import foundation.env as env
 from dna.model.DnaStrandOrSegment import DnaStrandOrSegment
 from dna.model.DnaLadderRailChunk import DnaAxisChunk
 
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 from model.chunk import Chunk
 from model.chem import Atom
 from model.bonds import Bond
 from geometry.VQT import V, norm, vlen
 from dna.model.Dna_Constants import getDuplexRiseFromNumberOfBasePairs
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 class DnaSegment(DnaStrandOrSegment):
     """
diff --git a/cad/src/dna/model/DnaStrand.py b/cad/src/dna/model/DnaStrand.py
index 27480e4e4..13684e691 100644
--- a/cad/src/dna/model/DnaStrand.py
+++ b/cad/src/dna/model/DnaStrand.py
@@ -14,12 +14,12 @@ import re
 
 from dna.model.DnaStrandOrSegment import DnaStrandOrSegment
 from dna.model.DnaLadderRailChunk import DnaStrandChunk
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 from dna.model.Dna_Constants import getComplementSequence
 
-from bond_chains import grow_directional_bond_chain
+from operations.bond_chains import grow_directional_bond_chain
 
 class DnaStrand(DnaStrandOrSegment):
     """
diff --git a/cad/src/dna/model/Dna_Constants.py b/cad/src/dna/model/Dna_Constants.py
index 2fed15c10..863540cca 100644
--- a/cad/src/dna/model/Dna_Constants.py
+++ b/cad/src/dna/model/Dna_Constants.py
@@ -22,11 +22,11 @@ History:
 """
 
 import foundation.env as env
-from constants import purple, brass, steelblue, lightgreen, darkgray, lightblue
-from constants import darkorange, violet, copper, olive, gray
-from prefs_constants import adnaBasesPerTurn_prefs_key, adnaRise_prefs_key
-from prefs_constants import bdnaBasesPerTurn_prefs_key, bdnaRise_prefs_key
-from prefs_constants import zdnaBasesPerTurn_prefs_key, zdnaRise_prefs_key
+from utilities.constants import purple, brass, steelblue, lightgreen, darkgray, lightblue
+from utilities.constants import darkorange, violet, copper, olive, gray
+from utilities.prefs_constants import adnaBasesPerTurn_prefs_key, adnaRise_prefs_key
+from utilities.prefs_constants import bdnaBasesPerTurn_prefs_key, bdnaRise_prefs_key
+from utilities.prefs_constants import zdnaBasesPerTurn_prefs_key, zdnaRise_prefs_key
 from PyQt4.Qt import QString
 
 basesDict = \
diff --git a/cad/src/dna/model/WholeChain.py b/cad/src/dna/model/WholeChain.py
index 4c4ac3738..df60d6b27 100644
--- a/cad/src/dna/model/WholeChain.py
+++ b/cad/src/dna/model/WholeChain.py
@@ -16,7 +16,7 @@ from dna.model.DnaMarker import DnaMarker # for isinstance
 from dna.model.DnaMarker import DnaSegmentMarker # constructor
 from dna.model.DnaMarker import DnaStrandMarker # constructor
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 class WholeChain(object):
     """
diff --git a/cad/src/dna/operations/crossovers.py b/cad/src/dna/operations/crossovers.py
index a3f96c2aa..268408169 100755
--- a/cad/src/dna/operations/crossovers.py
+++ b/cad/src/dna/operations/crossovers.py
@@ -16,7 +16,7 @@ TODO: make it work for PAM3 as well as PAM5.
 # - Pl position is wrong after either op, esp. Remove
 # - Undo and Feature Help cmdnames are wrong (not working)
 
-from constants import noop, average_value
+from utilities.constants import noop, average_value
 from model.bond_constants import V_SINGLE
 from model.bond_constants import atoms_are_bonded, find_bond
 from model.bonds import bond_atoms_faster, bond_direction ##, bond_atoms
diff --git a/cad/src/dna/temporary_commands/DnaLineMode.py b/cad/src/dna/temporary_commands/DnaLineMode.py
index edfcc9c9a..7f9c482e5 100644
--- a/cad/src/dna/temporary_commands/DnaLineMode.py
+++ b/cad/src/dna/temporary_commands/DnaLineMode.py
@@ -9,12 +9,12 @@ TODO:
 - User Preferences for different rubberband line display styles 
 """
 
-from LineMode import LineMode
+from temporary_commands.LineMode import LineMode
 
 from graphics.drawing.drawDnaLadder import drawDnaLadder
 from graphics.drawing.drawDnaRibbons import drawDnaRibbons
 
-from constants import black, darkred, blue, white
+from utilities.constants import black, darkred, blue, white
 
 # == GraphicsMode part
 
diff --git a/cad/src/dna/updater/dna_updater_atoms.py b/cad/src/dna/updater/dna_updater_atoms.py
index 003c7834d..a85306572 100644
--- a/cad/src/dna/updater/dna_updater_atoms.py
+++ b/cad/src/dna/updater/dna_updater_atoms.py
@@ -7,7 +7,7 @@ dna_updater_atoms.py - enforce rules on newly changed PAM atoms and bonds
 @copyright: 2007-2008 Nanorex, Inc.  See LICENSE file for details.
 """
 
-from constants import noop as STUB_FUNCTION # FIX all uses
+from utilities.constants import noop as STUB_FUNCTION # FIX all uses
 
 from dna.updater.dna_updater_globals import get_changes_and_clear
 from dna.updater.dna_updater_globals import ignore_new_changes
diff --git a/cad/src/dna/updater/dna_updater_commands.py b/cad/src/dna/updater/dna_updater_commands.py
index 9c45082e0..6fcdbb122 100644
--- a/cad/src/dna/updater/dna_updater_commands.py
+++ b/cad/src/dna/updater/dna_updater_commands.py
@@ -7,7 +7,7 @@ dna_updater_commands.py - UI commands offered directly by the dna updater.
 @copyright: 2007-2008 Nanorex, Inc.  See LICENSE file for details.
 """
 
-from debug import register_debug_menu_command
+from utilities.debug import register_debug_menu_command
 
 from model.chem import _changed_structure_Atoms # but it's private! refactor sometime
 
diff --git a/cad/src/dna/updater/dna_updater_debug.py b/cad/src/dna/updater/dna_updater_debug.py
index c8c9ce472..6ec153c81 100644
--- a/cad/src/dna/updater/dna_updater_debug.py
+++ b/cad/src/dna/updater/dna_updater_debug.py
@@ -17,11 +17,11 @@ import foundation.env as env
 
 from utilities.Log import quote_html
 
-from debug import register_debug_menu_command
+from utilities.debug import register_debug_menu_command
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
-from constants import gensym
+from utilities.constants import gensym
 
 from widgets.simple_dialogs import grab_text_using_dialog
 
diff --git a/cad/src/dna/updater/dna_updater_find_chains.py b/cad/src/dna/updater/dna_updater_find_chains.py
index 5374d8de1..0d27a630d 100644
--- a/cad/src/dna/updater/dna_updater_find_chains.py
+++ b/cad/src/dna/updater/dna_updater_find_chains.py
@@ -9,14 +9,14 @@ dna_updater_find_chains.py - helper for dna_updater_chunks
 
 from utilities import debug_flags
 
-from bond_chains import abstract_bond_chain_analyzer
+from operations.bond_chains import abstract_bond_chain_analyzer
 
 from dna.model.AtomChainOrRing import AtomChain, AtomRing
 
 from dna.model.DnaChain import AxisChain, StrandChain
 from dna.model.DnaChain import DnaChain_AtomChainWrapper # for isinstance
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 # ==
 
diff --git a/cad/src/dna/updater/dna_updater_follow_strand.py b/cad/src/dna/updater/dna_updater_follow_strand.py
index fd012968d..c03b722a2 100644
--- a/cad/src/dna/updater/dna_updater_follow_strand.py
+++ b/cad/src/dna/updater/dna_updater_follow_strand.py
@@ -7,7 +7,7 @@ dna_updater_follow_strand.py - helper function for dna_updater_ladders.
 @copyright: 2007-2008 Nanorex, Inc.  See LICENSE file for details.
 """
 
-from constants import noop
+from utilities.constants import noop
 
 _FAKE_AXIS_FOR_BARE_STRANDS = [1]
     # arbitrary non-false object comparable using 'is'
diff --git a/cad/src/dna/updater/dna_updater_globals.py b/cad/src/dna/updater/dna_updater_globals.py
index 0f3b0585f..b32c04cdf 100644
--- a/cad/src/dna/updater/dna_updater_globals.py
+++ b/cad/src/dna/updater/dna_updater_globals.py
@@ -15,7 +15,7 @@ from foundation.changedicts import _cdproc_for_dictid # but it's private!
 
 from model.chem import _changed_structure_Atoms, _changed_parent_Atoms # but they're private! refactor sometime
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 _DEBUG_ATOM_KEY = None # None, or a value of atom.key for which all ignored changes should be printed
 
diff --git a/cad/src/dna/updater/dna_updater_prefs.py b/cad/src/dna/updater/dna_updater_prefs.py
index 6c3c4bc85..bd098d2a8 100644
--- a/cad/src/dna/updater/dna_updater_prefs.py
+++ b/cad/src/dna/updater/dna_updater_prefs.py
@@ -7,8 +7,8 @@ dna_updater_prefs.py - access to preferences settings affecting the dna updater
 @copyright: 2007-2008 Nanorex, Inc.  See LICENSE file for details.
 """
 
-from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
-from debug_prefs import Choice
+from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+from utilities.debug_prefs import Choice
 
 import foundation.env as env
 
diff --git a/cad/src/dna/updater/fix_bond_directions.py b/cad/src/dna/updater/fix_bond_directions.py
index 271d1099c..d5822b942 100644
--- a/cad/src/dna/updater/fix_bond_directions.py
+++ b/cad/src/dna/updater/fix_bond_directions.py
@@ -11,7 +11,7 @@ from model.elements import Singlet
 
 import foundation.env as env
 from utilities.Log import orangemsg
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
 from dna.updater.dna_updater_prefs import pref_print_bond_direction_errors
 
diff --git a/cad/src/dna/updater/fix_deprecated_elements.py b/cad/src/dna/updater/fix_deprecated_elements.py
index 56eadef18..641f7e19c 100644
--- a/cad/src/dna/updater/fix_deprecated_elements.py
+++ b/cad/src/dna/updater/fix_deprecated_elements.py
@@ -9,7 +9,7 @@ fix_deprecated_elements.py - fix deprecated PAM elements in-place in models
 
 from model.elements import PeriodicTable
 
-from constants import diDEFAULT
+from utilities.constants import diDEFAULT
 
 from utilities import debug_flags
 
diff --git a/cad/src/exprs/Arrow.py b/cad/src/exprs/Arrow.py
index b65c056d2..eb298ad1e 100644
--- a/cad/src/exprs/Arrow.py
+++ b/cad/src/exprs/Arrow.py
@@ -12,7 +12,7 @@ from exprs.widget2d import Widget2D
 from exprs.attr_decl_macros import ArgOrOption
 from exprs.ExprsConstants import Color, Position, ORIGIN, DX
 
-from constants import gray
+from utilities.constants import gray
 
 from graphics.drawing.drawer import drawDirectionArrow 
 
diff --git a/cad/src/exprs/Boxed.py b/cad/src/exprs/Boxed.py
index 53a64786d..1143148b2 100755
--- a/cad/src/exprs/Boxed.py
+++ b/cad/src/exprs/Boxed.py
@@ -10,7 +10,7 @@ See also: DraggablyBoxed
 
 """
 
-from constants import white
+from utilities.constants import white
 
 from exprs.Rect import RectFrame
 from exprs.Overlay import Overlay
diff --git a/cad/src/exprs/DisplayListChunk.py b/cad/src/exprs/DisplayListChunk.py
index b85695a3f..f592fb295 100755
--- a/cad/src/exprs/DisplayListChunk.py
+++ b/cad/src/exprs/DisplayListChunk.py
@@ -50,9 +50,9 @@ just pointers to the draw-method-owning parents in each one, to be stored in the
 
 from OpenGL.GL import GL_COMPILE
 
-from debug_prefs import Choice_boolean_False
-from debug_prefs import debug_pref
-from debug import print_compact_traceback
+from utilities.debug_prefs import Choice_boolean_False
+from utilities.debug_prefs import debug_pref
+from utilities.debug import print_compact_traceback
 
 from foundation.changes import SelfUsageTrackingMixin # defines track_use, track_inval; maintains a private __subslist on self
 from foundation.changes import SubUsageTrackingMixin # defines begin_tracking_usage, end_tracking_usage; doesn't use self
diff --git a/cad/src/exprs/DraggableHandle.py b/cad/src/exprs/DraggableHandle.py
index 4e3884351..6fb7557ce 100644
--- a/cad/src/exprs/DraggableHandle.py
+++ b/cad/src/exprs/DraggableHandle.py
@@ -11,7 +11,7 @@ to avoid confusion with the DragHandler API (which would
 otherwise differ by only the final 'r').
 """
 
-from constants import white
+from utilities.constants import white
 
 from exprs.attr_decl_macros import Instance, Option
 from exprs.transforms import Translate
diff --git a/cad/src/exprs/DraggableHandle_AlongCircle.py b/cad/src/exprs/DraggableHandle_AlongCircle.py
index 617b12a1a..3bd2be057 100644
--- a/cad/src/exprs/DraggableHandle_AlongCircle.py
+++ b/cad/src/exprs/DraggableHandle_AlongCircle.py
@@ -3,7 +3,7 @@
 $Id$
 """
 
-from constants import white
+from utilities.constants import white
 
 from exprs.attr_decl_macros import Instance, Option
 from exprs.transforms import Translate
diff --git a/cad/src/exprs/Exprs.py b/cad/src/exprs/Exprs.py
index 99a3a5c9c..9cfede9c9 100755
--- a/cad/src/exprs/Exprs.py
+++ b/cad/src/exprs/Exprs.py
@@ -14,9 +14,9 @@ this file is getting kind of long - maybe split it in some sensible way?
 # note: this module should not import ExprsMeta, though its InstanceOrExpr subclass needs to (in another module).
 # instead, it is probably fully imported by ExprsMeta.
 
-from debug import compact_stack
-from debug import print_compact_stack
-from debug import safe_repr
+from utilities.debug import compact_stack
+from utilities.debug import print_compact_stack
+from utilities.debug import safe_repr
 
 ##from debug_prefs import debug_pref, Choice_boolean_False, Choice_boolean_True, Choice
 
diff --git a/cad/src/exprs/ExprsConstants.py b/cad/src/exprs/ExprsConstants.py
index da7165330..10a01c726 100644
--- a/cad/src/exprs/ExprsConstants.py
+++ b/cad/src/exprs/ExprsConstants.py
@@ -15,10 +15,10 @@ from geometry.VQT import V
 
 # compass positions, also usable for DrawInCorner
 
-from prefs_constants import UPPER_RIGHT
-from prefs_constants import UPPER_LEFT 
-from prefs_constants import LOWER_LEFT 
-from prefs_constants import LOWER_RIGHT
+from utilities.prefs_constants import UPPER_RIGHT
+from utilities.prefs_constants import UPPER_LEFT 
+from utilities.prefs_constants import LOWER_LEFT 
+from utilities.prefs_constants import LOWER_RIGHT
 
     # note: their values are ints -- perhaps hard to change since they might correspond to Qt radiobutton indices (guess)
 
@@ -63,12 +63,12 @@ nevermind = lambda func: identity
 
 #e maybe import the following from a different file, but for now we need to define some here
 #k need to make sure none of these are defined elsewhere in this module
-from constants import red, green, blue, white
+from utilities.constants import red, green, blue, white
 ##from constants import black, purple, magenta, violet, yellow, orange, pink, gray
     # note: various defs of purple I've seen:
     # ave_colors( 0.5, red, blue), or (0.5, 0.0, 0.5), or (0.7,0.0,0.7), or (0.6, 0.1, 0.9) == violet in constants.py
 ##from constants import aqua, darkgreen, navy, darkred, lightblue
-from constants import ave_colors
+from utilities.constants import ave_colors
     ###e what does this do to alpha? A: uses zip, which means, weight it if present in both colors, discard it otherwise.
     ###k What *should* it do? Not that, but that is at least not going to cause "crashes" in non-alpha-using code.
 
diff --git a/cad/src/exprs/ExprsMeta.py b/cad/src/exprs/ExprsMeta.py
index 6a702c3bb..68c19a29b 100755
--- a/cad/src/exprs/ExprsMeta.py
+++ b/cad/src/exprs/ExprsMeta.py
@@ -138,9 +138,9 @@ from idlelib.Delegator import Delegator
 
 # from modules in cad/src
 
-from constants import remove_prefix
+from utilities.constants import remove_prefix
 ##from env import seen_before
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 
 # from this exprs package in cad/src
 
diff --git a/cad/src/exprs/Highlightable.py b/cad/src/exprs/Highlightable.py
index d4879334e..1cd7de050 100755
--- a/cad/src/exprs/Highlightable.py
+++ b/cad/src/exprs/Highlightable.py
@@ -45,9 +45,9 @@ from utilities import debug_flags
 from geometry.VQT import A
 from geometry.VQT import vlen
 from geometry.VQT import V
-from constants import noop
-from constants import green
-from debug import print_compact_traceback
+from utilities.constants import noop
+from utilities.constants import green
+from utilities.debug import print_compact_traceback
 
 from exprs.Exprs import or_Expr, canon_expr
 from exprs.Exprs import printfunc
diff --git a/cad/src/exprs/If_expr.py b/cad/src/exprs/If_expr.py
index 841c36bfb..e62f1aef6 100755
--- a/cad/src/exprs/If_expr.py
+++ b/cad/src/exprs/If_expr.py
@@ -12,7 +12,7 @@ but for now, it has to be in this separate file (maybe that's best anyway).
 Note: file needs cleanup, and code needs reimplem.
 """
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 from exprs.Exprs import OpExpr, canon_expr, expr_constant_value
 from exprs.instance_helpers import InstanceMacro
diff --git a/cad/src/exprs/IorE_guest_mixin.py b/cad/src/exprs/IorE_guest_mixin.py
index ef79a7c7f..871b9e163 100644
--- a/cad/src/exprs/IorE_guest_mixin.py
+++ b/cad/src/exprs/IorE_guest_mixin.py
@@ -14,8 +14,8 @@ from exprs.lvals import call_but_discard_tracked_usage
 
 from exprs.widget_env import thisname_of_class, widget_env
 
-from debug import safe_repr
-from debug import print_compact_stack
+from utilities.debug import safe_repr
+from utilities.debug import print_compact_stack
 
 from exprs.Exprs import Expr
 from exprs.Exprs import is_pure_expr
diff --git a/cad/src/exprs/Rect.py b/cad/src/exprs/Rect.py
index 09a3af289..c2f743ef9 100755
--- a/cad/src/exprs/Rect.py
+++ b/cad/src/exprs/Rect.py
@@ -21,7 +21,7 @@ from OpenGL.GLU import gluPartialDisk
 
 from utilities import debug_flags
 
-from constants import gray, white, black
+from utilities.constants import gray, white, black
 
 from exprs.widget2d import Widget2D
 from exprs.attr_decl_macros import Arg, ArgOrOption, Option
diff --git a/cad/src/exprs/controls.py b/cad/src/exprs/controls.py
index 193f386a4..206e0e7bb 100755
--- a/cad/src/exprs/controls.py
+++ b/cad/src/exprs/controls.py
@@ -50,9 +50,9 @@ from exprs.staterefs import LocalVariable_StateRef ###e move to basic, if it doe
 
 ##from exprs.debug_exprs import debug_evals_of_Expr
 
-from constants import gray, blue, yellow, orange
-from debug_prefs import debug_pref
-from debug_prefs import Choice_boolean_False
+from utilities.constants import gray, blue, yellow, orange
+from utilities.debug_prefs import debug_pref
+from utilities.debug_prefs import Choice_boolean_False
 
 from exprs.widget2d import Widget2D
 from exprs.Exprs import format_Expr, eq_Expr, not_Expr, call_Expr, or_Expr
diff --git a/cad/src/exprs/debug_exprs.py b/cad/src/exprs/debug_exprs.py
index 4f3108a2a..e691ff069 100755
--- a/cad/src/exprs/debug_exprs.py
+++ b/cad/src/exprs/debug_exprs.py
@@ -5,8 +5,8 @@ $Id$
 
 # == local imports with reload
 
-from debug import safe_repr
-from debug import print_compact_stack
+from utilities.debug import safe_repr
+from utilities.debug import print_compact_stack
 
 from exprs.Exprs import internal_Expr ###k probably not needed (imported by basic) but needs test
 
diff --git a/cad/src/exprs/demo_MT.py b/cad/src/exprs/demo_MT.py
index 2271799b4..ee0f8265e 100755
--- a/cad/src/exprs/demo_MT.py
+++ b/cad/src/exprs/demo_MT.py
@@ -117,10 +117,10 @@ nfrs:
 
 # == imports
 
-from constants import blue, green, ave_colors, white
+from utilities.constants import blue, green, ave_colors, white
 
-from debug import print_compact_traceback
-from debug import safe_repr
+from utilities.debug import print_compact_traceback
+from utilities.debug import safe_repr
 
 from exprs.Highlightable import Highlightable
 from exprs.TextRect import TextRect
diff --git a/cad/src/exprs/demo_drag.py b/cad/src/exprs/demo_drag.py
index 8cce80809..48c616674 100755
--- a/cad/src/exprs/demo_drag.py
+++ b/cad/src/exprs/demo_drag.py
@@ -54,12 +54,12 @@ from exprs.DisplayListChunk import DisplayListChunk
 
 from exprs.world import World
 
-from constants import black, noop
-from constants import red
-from constants import blue
-from constants import green
-from constants import white
-from constants import yellow
+from utilities.constants import black, noop
+from utilities.constants import red
+from utilities.constants import blue
+from utilities.constants import green
+from utilities.constants import white
+from utilities.constants import yellow
 
 from exprs.Exprs import list_Expr, eval_Expr, call_Expr
 from exprs.Exprs import mod_Expr
diff --git a/cad/src/exprs/demo_draw_on_surface.py b/cad/src/exprs/demo_draw_on_surface.py
index 66fa3b513..46d07afb7 100755
--- a/cad/src/exprs/demo_draw_on_surface.py
+++ b/cad/src/exprs/demo_draw_on_surface.py
@@ -21,7 +21,7 @@ from OpenGL.GL import GL_LINE_STRIP
 from OpenGL.GL import glVertex3fv
 from OpenGL.GL import glEnd
 
-from constants import yellow, purple, red, noop
+from utilities.constants import yellow, purple, red, noop
 
 from widgets.simple_dialogs import grab_text_using_dialog
 
diff --git a/cad/src/exprs/demo_polyline.py b/cad/src/exprs/demo_polyline.py
index df83c4ee4..85f6e7e50 100755
--- a/cad/src/exprs/demo_polyline.py
+++ b/cad/src/exprs/demo_polyline.py
@@ -33,7 +33,7 @@ from OpenGL.GL import GL_LINE_STRIP
 from OpenGL.GL import glVertex3fv
 from OpenGL.GL import glEnd
 
-from constants import blue, noop
+from utilities.constants import blue, noop
 
 from exprs.Exprs import list_Expr, call_Expr
 from exprs.instance_helpers import DelegatingInstanceOrExpr, ModelObject
diff --git a/cad/src/exprs/demo_ui.py b/cad/src/exprs/demo_ui.py
index 0abdce27c..9eee86d46 100755
--- a/cad/src/exprs/demo_ui.py
+++ b/cad/src/exprs/demo_ui.py
@@ -11,8 +11,8 @@ from exprs.toolbars import MainToolbar
 
 from exprs.command_registry import find_or_make_global_command_registry
 
-from constants import pink
-from prefs_constants import UPPER_LEFT, UPPER_RIGHT
+from utilities.constants import pink
+from utilities.prefs_constants import UPPER_LEFT, UPPER_RIGHT
 
 from exprs.Exprs import list_Expr
 from exprs.If_expr import If
diff --git a/cad/src/exprs/dna_ribbon_view.py b/cad/src/exprs/dna_ribbon_view.py
index c94e68d88..79cceffc3 100755
--- a/cad/src/exprs/dna_ribbon_view.py
+++ b/cad/src/exprs/dna_ribbon_view.py
@@ -129,10 +129,10 @@ from exprs.pallettes import PalletteWell
 
 from geometry.VQT import norm
 
-from constants import gray, black, red, blue, purple, white
-from constants import ave_colors, noop
-from constants import green
-from constants import yellow
+from utilities.constants import gray, black, red, blue, purple, white
+from utilities.constants import ave_colors, noop
+from utilities.constants import green
+from utilities.constants import yellow
 
 from exprs.widget2d import Widget, Stub
 from exprs.Exprs import norm_Expr, vlen_Expr, int_Expr, call_Expr, getattr_Expr, format_Expr
diff --git a/cad/src/exprs/draggable.py b/cad/src/exprs/draggable.py
index 31a57300c..710cc36e4 100755
--- a/cad/src/exprs/draggable.py
+++ b/cad/src/exprs/draggable.py
@@ -70,7 +70,7 @@ from geometry.VQT import V, Q
 from geometry.VQT import norm
 from geometry.VQT import cross
 from geometry.VQT import vlen
-from constants import blue, white, ave_colors
+from utilities.constants import blue, white, ave_colors
 
 from exprs.Exprs import call_Expr, LvalueFromObjAndAttr, format_Expr, V_expr, neg_Expr
 from exprs.Boxed import Boxed
diff --git a/cad/src/exprs/images.py b/cad/src/exprs/images.py
index c0ce395f0..a8511c7aa 100755
--- a/cad/src/exprs/images.py
+++ b/cad/src/exprs/images.py
@@ -99,7 +99,7 @@ import graphics.drawing.texture_helpers as texture_helpers
     #   function create_PIL_image_obj_from_image_file, a trivial glue function into ImageUtils.py class nEImageOps,
     #   function loadTexture.
 
-from icon_utilities import image_directory # for finding texture & cursor files
+from utilities.icon_utilities import image_directory # for finding texture & cursor files
 
 # last-resort image file (same image file is used in other modules, but for different purposes)
 courierfile = os.path.join( image_directory(), "ui/exprs/text/courier-128.png") ### TODO: RENAME
@@ -254,13 +254,13 @@ def canon_image_filename( filename):
 ##    #stub, might work for now:
 ##    thisdir = os.path.dirname(__file__) # dir of exprs module
 ##    CAD_SRC_PATH = os.path.dirname( thisdir)
-    from constants import CAD_SRC_PATH
+    from utilities.constants import CAD_SRC_PATH
         # [note: in a built Mac release, this might be Contents/Resources/Python/site-packages.zip, or
         #  a related pathname; see comments near its definition.]
     cad = os.path.dirname( CAD_SRC_PATH) # used below for cad/images
 
     # image file path extensively revised 070604, mainly so testmode can work in a built release package
-    from PlatformDependent import path_of_Nanorex_subdir
+    from platform.PlatformDependent import path_of_Nanorex_subdir
 
     # main exprs-package image directory
     cad_src_ui_exprs = os.path.join( image_directory(), "ui/exprs") # not necessarily really in cad/src (in a built release)
diff --git a/cad/src/exprs/instance_helpers.py b/cad/src/exprs/instance_helpers.py
index d5ea24661..dd99d6925 100755
--- a/cad/src/exprs/instance_helpers.py
+++ b/cad/src/exprs/instance_helpers.py
@@ -17,8 +17,8 @@ from exprs.lvals import LvalError_ValueIsUnset
 
 from exprs.widget_env import thisname_of_class, widget_env #e refile import?? or make it an env method??
 
-from debug import print_compact_traceback
-from debug import print_compact_stack
+from utilities.debug import print_compact_traceback
+from utilities.debug import print_compact_stack
 
 from exprs.Exprs import is_pure_expr
 from exprs.Exprs import is_expr_Instance
diff --git a/cad/src/exprs/lvals.py b/cad/src/exprs/lvals.py
index 843804ecf..135385991 100755
--- a/cad/src/exprs/lvals.py
+++ b/cad/src/exprs/lvals.py
@@ -61,7 +61,7 @@ import sys
 
 from foundation.changes import SelfUsageTrackingMixin, SubUsageTrackingMixin
 import foundation.changes as changes
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from utilities.Comparison import same_vals
 
 ##from utilities import debug_flags
diff --git a/cad/src/exprs/outtakes/basic.py b/cad/src/exprs/outtakes/basic.py
index 6235a38c7..b47cfce8e 100755
--- a/cad/src/exprs/outtakes/basic.py
+++ b/cad/src/exprs/outtakes/basic.py
@@ -48,11 +48,11 @@ from math import pi, sin, cos #070130
 from foundation.state_utils import transclose, same_vals
 ## not yet needed: from state_utils import _UNSET_ # warning: not included in "import *"
 
-from constants import noop # def noop(*args,**kws): pass
+from utilities.constants import noop # def noop(*args,**kws): pass
 
-from debug import print_compact_traceback, print_compact_stack, safe_repr
+from utilities.debug import print_compact_traceback, print_compact_stack, safe_repr
 
-from debug_prefs import debug_pref, Choice_boolean_False, Choice_boolean_True, Choice #070228
+from utilities.debug_prefs import debug_pref, Choice_boolean_False, Choice_boolean_True, Choice #070228
 
 # consider also doing: import env as global_env  [070313 suggestion]
 
diff --git a/cad/src/exprs/pallettes.py b/cad/src/exprs/pallettes.py
index 47015a024..6dbca1ebb 100755
--- a/cad/src/exprs/pallettes.py
+++ b/cad/src/exprs/pallettes.py
@@ -14,7 +14,7 @@ from exprs.Boxed import Boxed
 
 from exprs.draggable import DraggableObject
 
-from constants import blue, green
+from utilities.constants import blue, green
 
 from exprs.Exprs import or_Expr, format_Expr
 from exprs.instance_helpers import DelegatingInstanceOrExpr
diff --git a/cad/src/exprs/projection.py b/cad/src/exprs/projection.py
index 8245f9768..b02f0cd16 100755
--- a/cad/src/exprs/projection.py
+++ b/cad/src/exprs/projection.py
@@ -25,7 +25,7 @@ except:
     # The installed version of OpenGL requires argument-typed glScale calls.
     glScale = glScalef
 
-from prefs_constants import UPPER_RIGHT, UPPER_LEFT, LOWER_LEFT, LOWER_RIGHT # note: also in basic.py as of 070302
+from utilities.prefs_constants import UPPER_RIGHT, UPPER_LEFT, LOWER_LEFT, LOWER_RIGHT # note: also in basic.py as of 070302
 
 from exprs.attr_decl_macros import Arg, ArgOrOption, Option
 from exprs.instance_helpers import DelegatingInstanceOrExpr
diff --git a/cad/src/exprs/reload.py b/cad/src/exprs/reload.py
index 2b993e38b..f5fcfd96e 100644
--- a/cad/src/exprs/reload.py
+++ b/cad/src/exprs/reload.py
@@ -9,8 +9,8 @@ Note: as of 070921 reload_once is no longer called except in testdraw.py.
 """
 
 from utilities import debug_flags
-import EndUser
-from debug import reload_once_per_event
+import utilities.EndUser as EndUser
+from utilities.debug import reload_once_per_event
 
 ENABLE_RELOAD = True and debug_flags.atom_debug
 
diff --git a/cad/src/exprs/scratch/ModelNode.py b/cad/src/exprs/scratch/ModelNode.py
index 99c86596d..b22917f07 100755
--- a/cad/src/exprs/scratch/ModelNode.py
+++ b/cad/src/exprs/scratch/ModelNode.py
@@ -68,7 +68,7 @@ from exprs.lvals import RecomputingMemoDict ##, call_but_discard_tracked_usage,
 
 import foundation.env as env
 
-from constants import gray
+from utilities.constants import gray
 
 from exprs.instance_helpers import InstanceOrExpr
 from exprs.attr_decl_macros import StateArg, StateArgOrOption, Arg
diff --git a/cad/src/exprs/scratch/PixelTester.py b/cad/src/exprs/scratch/PixelTester.py
index 53fdddcf6..bd84b5f85 100755
--- a/cad/src/exprs/scratch/PixelTester.py
+++ b/cad/src/exprs/scratch/PixelTester.py
@@ -17,7 +17,7 @@ $Id$
 
 #e more imports
 
-from constants import blue, purple
+from utilities.constants import blue, purple
 
 from exprs.widget2d import Widget2D
 from exprs.Exprs import format_Expr
diff --git a/cad/src/exprs/scratch/test_animation_mode.py b/cad/src/exprs/scratch/test_animation_mode.py
index b3330d4fb..391ad2058 100644
--- a/cad/src/exprs/scratch/test_animation_mode.py
+++ b/cad/src/exprs/scratch/test_animation_mode.py
@@ -46,11 +46,11 @@ and a couple more noted on g4:
 - a few more
 """
 
-from prefs_widgets import Preferences_StateRef, Preferences_StateRef_double, ObjAttr_StateRef
+from widgets.prefs_widgets import Preferences_StateRef, Preferences_StateRef_double, ObjAttr_StateRef
 from foundation.changes import Formula
 
 ## from test_animation_mode_PM import test_animation_mode_PM
-from test_command_PMs import ExampleCommand1_PM
+from prototype.test_command_PMs import ExampleCommand1_PM
 from PM.PM_GroupBox import PM_GroupBox
 from PM.PM_DoubleSpinBox import PM_DoubleSpinBox
 from PM.PM_PushButton import PM_PushButton
@@ -61,12 +61,12 @@ from PM.PM_CheckBox import PM_CheckBox
 from command_support.Command import Command
 from command_support.GraphicsMode import GraphicsMode
 
-from debug import print_compact_traceback, register_debug_menu_command
+from utilities.debug import print_compact_traceback, register_debug_menu_command
 import time, math
 
 from foundation.state_utils import copy_val
 
-from constants import green, red, white, pink, black, brown, gray # other colors below
+from utilities.constants import green, red, white, pink, black, brown, gray # other colors below
 from math import pi
 from graphics.drawing.drawer import drawline, drawbrick, drawsphere, drawcylinder
 from OpenGL.GL import GL_LIGHTING, glDisable, glEnable
@@ -968,7 +968,7 @@ annoyers = [##'editToolbar', 'fileToolbar', 'helpToolbar', 'modifyToolbar',
 # these imports are not needed in a minimal example like ExampleCommand2;
 # to make that clear, we put them down here instead of at the top of the file
 from graphics.drawing.drawer import drawline
-from constants import red, green
+from utilities.constants import red, green
 ##from exprs.ExprsConstants import PIXELS
 from exprs.images import Image
 ##from exprs.Overlay import Overlay
diff --git a/cad/src/exprs/test.py b/cad/src/exprs/test.py
index b84d18dac..69a7ac232 100755
--- a/cad/src/exprs/test.py
+++ b/cad/src/exprs/test.py
@@ -137,12 +137,12 @@ from exprs.test_statearray_3 import test_StateArrayRefs_3
 from geometry.VQT import V
 from utilities.Comparison import same_vals
 
-from constants import purple, white, blue, red, orange, green, lightgreen
-from constants import gray, pink, yellow, black
-from constants import ave_colors, noop
+from utilities.constants import purple, white, blue, red, orange, green, lightgreen
+from utilities.constants import gray, pink, yellow, black
+from utilities.constants import ave_colors, noop
 # more colors imported below, from ExprsConstants
 
-from prefs_constants import displayOriginAxis_prefs_key
+from utilities.prefs_constants import displayOriginAxis_prefs_key
 from graphics.drawing.texture_fonts import courierfile
 from exprs.reload import exprs_globals
 
diff --git a/cad/src/exprs/test_statearray.py b/cad/src/exprs/test_statearray.py
index 754b354dd..7722d052c 100755
--- a/cad/src/exprs/test_statearray.py
+++ b/cad/src/exprs/test_statearray.py
@@ -18,7 +18,7 @@ from exprs.Boxed import Boxed
 
 from exprs.Set import Set
 
-from constants import black, pink
+from utilities.constants import black, pink
 
 from exprs.Exprs import call_Expr
 from exprs.statearray import StateArrayRefs, StateArrayRefs_getitem_as_stateref
diff --git a/cad/src/exprs/test_statearray_3.py b/cad/src/exprs/test_statearray_3.py
index 96f89a048..326187092 100644
--- a/cad/src/exprs/test_statearray_3.py
+++ b/cad/src/exprs/test_statearray_3.py
@@ -36,7 +36,7 @@ from exprs.transforms import Translate
 
 from exprs.Overlay import Overlay
 
-from constants import white
+from utilities.constants import white
 
 from exprs.Exprs import call_Expr, tuple_Expr
 from exprs.statearray import StateArrayRefs, StateArrayRefs_getitem_as_stateref
diff --git a/cad/src/exprs/testdraw.py b/cad/src/exprs/testdraw.py
index 0eef5cdc6..e0d1058c3 100755
--- a/cad/src/exprs/testdraw.py
+++ b/cad/src/exprs/testdraw.py
@@ -83,13 +83,13 @@ from OpenGL.GL import glTranslate
 import foundation.env as env
 from utilities import debug_flags
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from constants import ave_colors
-from constants import blue
-from constants import white
-from constants import green
-from constants import red
+from utilities.constants import ave_colors
+from utilities.constants import blue
+from utilities.constants import white
+from utilities.constants import green
+from utilities.constants import red
 
 from exprs.reload import exprs_globals
     #bruce 071102 renamed vv -> exprs_globals and moved it out of this file,
diff --git a/cad/src/exprs/testmode.py b/cad/src/exprs/testmode.py
index 9b874f10d..29bf65eb1 100755
--- a/cad/src/exprs/testmode.py
+++ b/cad/src/exprs/testmode.py
@@ -36,10 +36,10 @@ import time
 from geometry.VQT import V, Q
 from commands.BuildAtoms.depositMode import depositMode
 
-from debug import print_compact_traceback
-from debug_prefs import Choice_boolean_True
-from debug_prefs import Choice_boolean_False
-from debug_prefs import debug_pref
+from utilities.debug import print_compact_traceback
+from utilities.debug_prefs import Choice_boolean_True
+from utilities.debug_prefs import Choice_boolean_False
+from utilities.debug_prefs import debug_pref
 
 
 annoyers = ['editToolbar', 'fileToolbar', 'helpToolbar', 'modifyToolbar',
diff --git a/cad/src/exprs/toolbars.py b/cad/src/exprs/toolbars.py
index 18e836370..8175162e9 100755
--- a/cad/src/exprs/toolbars.py
+++ b/cad/src/exprs/toolbars.py
@@ -19,7 +19,7 @@ from exprs.Boxed import Boxed
 
 from exprs.command_registry import CommandRegistry
 
-from constants import gray, white, blue, green
+from utilities.constants import gray, white, blue, green
 
 from exprs.Exprs import list_Expr, format_Expr
 from exprs.If_expr import If
diff --git a/cad/src/extensions.py b/cad/src/extensions.py
index 9d6013d36..c8da8688b 100755
--- a/cad/src/extensions.py
+++ b/cad/src/extensions.py
@@ -75,7 +75,7 @@ have_pyrex_test = False
 debug_pyrex_test = False ## was debug_flags.atom_debug, changed to 0 for A7 release by bruce 060419
 
 import foundation.env as env
-from debug import register_debug_menu_command, call_func_with_timing_histmsg, print_compact_traceback
+from utilities.debug import register_debug_menu_command, call_func_with_timing_histmsg, print_compact_traceback
 
 # I think it's safe for the following pyrex_test import to be attempted even by
 # source analysis tools which import single files. Either they'll have
diff --git a/cad/src/files/dpb_trajectory/moviefile.py b/cad/src/files/dpb_trajectory/moviefile.py
index 691e82732..39e9e8fdc 100755
--- a/cad/src/files/dpb_trajectory/moviefile.py
+++ b/cad/src/files/dpb_trajectory/moviefile.py
@@ -19,7 +19,7 @@ from struct import unpack # fyi: used for old-format header, no longer for delta
 ## from VQT import A
 from Numeric import array, Int8
 from utilities import debug_flags
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 import foundation.env as env
 
 def MovieFile(filename): #bruce 050913 removed history arg, since all callers passed env.history
diff --git a/cad/src/files/mmp/files_mmp.py b/cad/src/files/mmp/files_mmp.py
index 92149ca4b..44553a590 100755
--- a/cad/src/files/mmp/files_mmp.py
+++ b/cad/src/files/mmp/files_mmp.py
@@ -51,11 +51,11 @@ from foundation.Utility import Node
 from foundation.Group import Group
 from model.NamedView import NamedView # for reading one, and for isinstance
 
-from debug import print_compact_traceback
-from debug import print_compact_stack
+from utilities.debug import print_compact_traceback
+from utilities.debug import print_compact_stack
 
-from constants import gensym
-from constants import dispNames
+from utilities.constants import gensym
+from utilities.constants import dispNames
 
 from model.bond_constants import find_bond
 from model.bond_constants import V_SINGLE
diff --git a/cad/src/files/mmp/files_mmp_writing.py b/cad/src/files/mmp/files_mmp_writing.py
index 6ef0806c9..349963b8d 100755
--- a/cad/src/files/mmp/files_mmp_writing.py
+++ b/cad/src/files/mmp/files_mmp_writing.py
@@ -115,9 +115,9 @@ MMP_FORMAT_VERSION_TO_WRITE = '050920 required; 080115 preferred'
 
 from utilities import debug_flags
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from constants import dispNames
+from utilities.constants import dispNames
 
 # ==
 
diff --git a/cad/src/files/pdb/files_pdb.py b/cad/src/files/pdb/files_pdb.py
index a5becce06..27d94d496 100755
--- a/cad/src/files/pdb/files_pdb.py
+++ b/cad/src/files/pdb/files_pdb.py
@@ -21,13 +21,13 @@ import os, time
 from model.chunk import Chunk
 from model.chem import Atom
 from model.bonds import bond_atoms
-from bonds_from_atoms import inferBonds
+from operations.bonds_from_atoms import inferBonds
 from string import capitalize
 from model.elements import PeriodicTable, Singlet
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from utilities.Log import redmsg, orangemsg
 from geometry.VQT import A
-from version import Version
+from utilities.version import Version
 from datetime import datetime
 import foundation.env as env
 
diff --git a/cad/src/foundation/Group.py b/cad/src/foundation/Group.py
index c0da09e9f..ea921f56f 100755
--- a/cad/src/foundation/Group.py
+++ b/cad/src/foundation/Group.py
@@ -18,13 +18,13 @@ split out Node and/or LeafNode as well.)
 Bruce 080305 changed superclass from Node to NodeWithAtomContents.
 """
 
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 from utilities import debug_flags
 import foundation.env as env
 from foundation.state_constants import S_CHILDREN
 
 from commands.GroupProperties.GroupProp import GroupProp
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 from foundation.NodeWithAtomContents import NodeWithAtomContents
 
@@ -548,7 +548,7 @@ class Group(NodeWithAtomContents):
             # so ob.pick() sees it's picked when its subr scans up the tree
         for ob in self.members:
             ob.pick()
-        from debug_prefs import debug_pref_History_print_every_selected_object
+        from utilities.debug_prefs import debug_pref_History_print_every_selected_object
         if debug_pref_History_print_every_selected_object(): #bruce 070504 added this condition
             # bruce 050131 comment:
             # I'm very skeptical of doing this history.message
diff --git a/cad/src/foundation/Utility.py b/cad/src/foundation/Utility.py
index 5e85a2865..d5e941daa 100755
--- a/cad/src/foundation/Utility.py
+++ b/cad/src/foundation/Utility.py
@@ -28,15 +28,15 @@ Bruce 080305 added some abstract classes between Node and Group
 in the inheritance hierarchy (defined in this module for now).
 """
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 from utilities import debug_flags
 import foundation.env as env
-from constants import genKey
+from utilities.constants import genKey
 from foundation.state_utils import copy_val, StateMixin, IdentityCopyMixin
 from utilities.Log import redmsg, orangemsg
 from foundation.state_constants import S_PARENT, S_DATA, S_CHILD
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 from foundation.Assembly_API import Assembly_API
 
diff --git a/cad/src/foundation/changedicts.py b/cad/src/foundation/changedicts.py
index b9faf833e..e365c9f1c 100755
--- a/cad/src/foundation/changedicts.py
+++ b/cad/src/foundation/changedicts.py
@@ -20,7 +20,7 @@ might be). [bruce 071106 comment]
 Update 071210: since that comment, it's also been used in the dna updater.
 """
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from foundation.changes import register_postinit_item
 
diff --git a/cad/src/foundation/changes.py b/cad/src/foundation/changes.py
index a0a34f6ad..473dfba76 100755
--- a/cad/src/foundation/changes.py
+++ b/cad/src/foundation/changes.py
@@ -22,9 +22,9 @@ bruce 071106 split changedicts.py out of changes.py
 
 """
 
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 import foundation.env as env
-from constants import noop
+from utilities.constants import noop
 from utilities import debug_flags
 from utilities.Comparison import same_vals #bruce 060306
 
diff --git a/cad/src/foundation/inval.py b/cad/src/foundation/inval.py
index a3cd45e05..0dae138fb 100755
--- a/cad/src/foundation/inval.py
+++ b/cad/src/foundation/inval.py
@@ -10,7 +10,7 @@ bruce 050513 replaced some == with 'is' and != with 'is not', to avoid __getattr
 on __xxx__ attrs in python objects.
 """
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 ##from debug import print_compact_stack
 
 debug_counter = 0 # uncomment the related code (far below) to find out what's calling our __getattr__ [bruce 050513]
diff --git a/cad/src/foundation/preferences.py b/cad/src/foundation/preferences.py
index a2610e630..32dc25ae3 100755
--- a/cad/src/foundation/preferences.py
+++ b/cad/src/foundation/preferences.py
@@ -62,15 +62,15 @@ import os
 import time
 
 from utilities import debug_flags
-from PlatformDependent import mkdirs_in_filename
-from PlatformDependent import find_or_make_Nanorex_directory
+from platform.PlatformDependent import mkdirs_in_filename
+from platform.PlatformDependent import find_or_make_Nanorex_directory
 import foundation.env as env
-import EndUser
-from debug import print_compact_traceback
+import utilities.EndUser as EndUser
+from utilities.debug import print_compact_traceback
 
 from foundation.changes import UsageTracker
 
-from prefs_constants import prefs_table
+from utilities.prefs_constants import prefs_table
 
 # some imports remain lower down, for now: bsddb and shelve
 
diff --git a/cad/src/foundation/state_utils.py b/cad/src/foundation/state_utils.py
index 2c4a5f4c9..84511fa04 100755
--- a/cad/src/foundation/state_utils.py
+++ b/cad/src/foundation/state_utils.py
@@ -28,12 +28,12 @@ from foundation.state_constants import ATOM_CHUNK_ATTRIBUTE_NAME
 from foundation.state_constants import _UNSET_, _Bugval
 
 import foundation.env as env
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 from utilities import debug_flags
 from utilities.Comparison import same_vals, SAMEVALS_SPEEDUP
-from constants import remove_prefix
+from utilities.constants import remove_prefix
 
-from GlobalPreferences import debug_pyrex_atoms
+from utilities.GlobalPreferences import debug_pyrex_atoms
 
 DEBUG_PYREX_ATOMS = debug_pyrex_atoms()
 
@@ -1681,7 +1681,7 @@ class obj_classifier:
 ##            self.kluge_attr2metainfo_from_class[attr] = clas # only for debugging
             if DEBUG_PYREX_ATOMS:
                 if not env.seen_before("DEBUG_PYREX_ATOMS"):
-                    from GlobalPreferences import usePyrexAtomsAndBonds
+                    from utilities.GlobalPreferences import usePyrexAtomsAndBonds
                     on = usePyrexAtomsAndBonds()
                     print "\nDEBUG_PYREX_ATOMS: Pyrex atoms is", on and "ON" or "OFF"
                     print
diff --git a/cad/src/foundation/undo_archive.py b/cad/src/foundation/undo_archive.py
index 123b6b324..ec8e38028 100755
--- a/cad/src/foundation/undo_archive.py
+++ b/cad/src/foundation/undo_archive.py
@@ -15,8 +15,8 @@ providing undo/redo ops which apply those diffs to the model state.
 
 import time
 from utilities import debug_flags
-from debug import print_compact_traceback, print_compact_stack, safe_repr
-from debug_prefs import debug_pref, Choice_boolean_False, Choice_boolean_True
+from utilities.debug import print_compact_traceback, print_compact_stack, safe_repr
+from utilities.debug_prefs import debug_pref, Choice_boolean_False, Choice_boolean_True
 import foundation.env as env
 
 import foundation.state_utils as state_utils
@@ -27,7 +27,7 @@ from foundation.state_constants import _UNSET_
 from foundation.state_constants import UNDO_SPECIALCASE_ATOM, UNDO_SPECIALCASE_BOND
 from foundation.state_constants import ATOM_CHUNK_ATTRIBUTE_NAME
 
-from prefs_constants import historyMsgSerialNumber_prefs_key
+from utilities.prefs_constants import historyMsgSerialNumber_prefs_key
 from foundation.changes import register_postinit_object
 import foundation.changedicts as changedicts # warning: very similar to some local variable names
 
@@ -1256,7 +1256,7 @@ def register_undo_updater( func, updates = (), after_update_of = () ):
     ## print "register_undo_updater ought to register %r but it's nim, or maybe only use of the registration is nim" % func
     # pseudocode
     if "pseudocode":
-        from constants import noop
+        from utilities.constants import noop
         somethingYouHaveToDo = progress_marker = canon = this_bfr_that = noop
     task = somethingYouHaveToDo(func)
     for name in updates:
diff --git a/cad/src/foundation/undo_internals.py b/cad/src/foundation/undo_internals.py
index ad209d060..9cb17af54 100755
--- a/cad/src/foundation/undo_internals.py
+++ b/cad/src/foundation/undo_internals.py
@@ -14,10 +14,10 @@ Module classification: foundation.
 """
 
 import foundation.env as env
-from debug import register_debug_menu_command
+from utilities.debug import register_debug_menu_command
 from PyQt4.Qt import QObject ## , QWidget, SIGNAL
 from utilities import debug_flags # for atom_debug
-import EndUser
+import utilities.EndUser as EndUser
 
 # debug print options
 
@@ -133,7 +133,7 @@ class wrappedslot:
             # Print a warning if it looks like the signal and slot argument counts don't match;
             # if DEBUG_GETARGSPEC then always print something about the analysis result.
             # Also try to save info on self, so args_info needn't be called at runtime.
-            from debug import print_compact_traceback
+            from utilities.debug import print_compact_traceback
             try:
                 self.args_info_result = args_info(slotboundmethod)
                 success, minargs, maxargs, any_kws_ok = self.args_info_result
@@ -244,7 +244,7 @@ class wrappedslot:
                             arglists_to_try.append(( args, kws ))
                     # Retry it with those arglists (zero or more of them to try)
                     worked = False
-                    from debug import print_compact_traceback
+                    from utilities.debug import print_compact_traceback
                     for args, kws in arglists_to_try:
                         try:
                             res = slotboundmethod(*args, **kws)
@@ -321,7 +321,7 @@ class wrappedslot:
                 # the leak per-cmenu is smaller than others we have per-user-command. ####@@@@ DOIT
             if fn:
                 if 1: #experiment 060121
-                    from debug import print_compact_traceback
+                    from utilities.debug import print_compact_traceback
                     try:
                         win = env.mainwindow()
                         assert win.initialised # make sure it's not too early
@@ -697,7 +697,7 @@ def args_info(func1): #bruce 071004 revised implem and return value format
         # TODO: there might be a smarter wrapper
         # for that function (which knows about bound methods specifically)
         # in some other introspection module.
-        from debug import print_compact_traceback
+        from utilities.debug import print_compact_traceback
         try:
             import inspect
             try:
diff --git a/cad/src/foundation/undo_manager.py b/cad/src/foundation/undo_manager.py
index 7d5f04bb1..baafa0f87 100755
--- a/cad/src/foundation/undo_manager.py
+++ b/cad/src/foundation/undo_manager.py
@@ -12,16 +12,16 @@ into a reasonable form for supporting a UI.
 [060117 -- for current status see undo_archive.py module docstring]
 """
 
-from debug import register_debug_menu_command_maker
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import register_debug_menu_command_maker
+from utilities.debug import print_compact_traceback, print_compact_stack
 
 from utilities import debug_flags
-from PlatformDependent import is_macintosh
+from platform.PlatformDependent import is_macintosh
 from foundation.undo_archive import AssyUndoArchive
 import foundation.undo_archive as undo_archive # for debug_undo2;
     # could move that to a debug flags module; not urgent
-from constants import noop
-from prefs_constants import undoAutomaticCheckpoints_prefs_key
+from utilities.constants import noop
+from utilities.prefs_constants import undoAutomaticCheckpoints_prefs_key
 import foundation.env as env
 from utilities.Log import greenmsg, redmsg ##, orangemsg
 import time
diff --git a/cad/src/foundation/whatsthis_utilities.py b/cad/src/foundation/whatsthis_utilities.py
index d2a73aba9..c2c12531c 100755
--- a/cad/src/foundation/whatsthis_utilities.py
+++ b/cad/src/foundation/whatsthis_utilities.py
@@ -69,7 +69,7 @@ def fix_whatsthis_text_and_links(parent, refix_later = (), debug_cutoff = 0):
         print "returning immediately (sanity check, bug better be there or"\
               "you're insane)" ####@@@@@ yes, bug is not fixed yet
         return
-    from PlatformDependent import is_macintosh
+    from platform.PlatformDependent import is_macintosh
     mac = is_macintosh()
     if mac or enable_whatsthis_links:
         # fix text in 1 or 2 ways for all QAction objects
@@ -215,7 +215,7 @@ def refix_whatsthis_text_and_links( ): #bruce 060319 part of fixing bug 1421
 ##        return
     import foundation.env as env
     win = env.mainwindow()
-    from PlatformDependent import is_macintosh
+    from platform.PlatformDependent import is_macintosh
     mac = is_macintosh()
     fix_QAction_whatsthis(win.editUndoAction, mac)
     fix_QAction_whatsthis(win.editRedoAction, mac)
diff --git a/cad/src/foundation/wiki_help.py b/cad/src/foundation/wiki_help.py
index 0832cd048..ed943e521 100755
--- a/cad/src/foundation/wiki_help.py
+++ b/cad/src/foundation/wiki_help.py
@@ -47,7 +47,7 @@ bruce 051201 made new source file for it, extended it to other kinds of objects
 from PyQt4 import QtGui
 from PyQt4.Qt import QDialog
 from PyQt4.Qt import QTextBrowser
-from NE1_QToolBar import NE1_QToolBar
+from widgets.NE1_QToolBar import NE1_QToolBar
 
 from PyQt4.Qt import QWhatsThisClickedEvent
 from PyQt4.Qt import QGridLayout
@@ -62,10 +62,10 @@ from PyQt4.Qt import SLOT
 import os
 import foundation.env as env
 import webbrowser
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from utilities.Log import redmsg
 ##from qt4transition import qt4todo
-from prefs_constants import wiki_help_prefix_prefs_key
+from utilities.prefs_constants import wiki_help_prefix_prefs_key
 
 def webbrowser_open(url):
     if len(webbrowser._tryorder) == 0:
diff --git a/cad/src/geometry/BoundingBox.py b/cad/src/geometry/BoundingBox.py
index 49a3e6b43..a4efde97e 100644
--- a/cad/src/geometry/BoundingBox.py
+++ b/cad/src/geometry/BoundingBox.py
@@ -24,7 +24,7 @@ from Numeric import add, subtract, sqrt
 from Numeric import maximum, minimum, dot
 
 from geometry.VQT import V, A, cat
-from constants import black
+from utilities.constants import black
 
 class BBox:
     """
diff --git a/cad/src/graphics/behaviors/Trackball.py b/cad/src/graphics/behaviors/Trackball.py
index 430fc69f9..85cedb8d7 100755
--- a/cad/src/graphics/behaviors/Trackball.py
+++ b/cad/src/graphics/behaviors/Trackball.py
@@ -13,7 +13,7 @@ Note: bruce 071216 moved class Trackball into its own file, from VQT.py.
 """
 
 import foundation.env as env
-from prefs_constants import mouseSpeedDuringRotation_prefs_key
+from utilities.prefs_constants import mouseSpeedDuringRotation_prefs_key
 
 from geometry.VQT import Q
 from geometry.VQT import proj2sphere
diff --git a/cad/src/graphics/behaviors/confirmation_corner.py b/cad/src/graphics/behaviors/confirmation_corner.py
index ed1db7717..f0d85ac42 100755
--- a/cad/src/graphics/behaviors/confirmation_corner.py
+++ b/cad/src/graphics/behaviors/confirmation_corner.py
@@ -32,9 +32,9 @@ from exprs.Rect import Rect # needed for Image size option, not just for testing
 ##from constants import green # only for testing
 
 from exprs.projection import DrawInCorner ##, DrawInCorner_projection
-from prefs_constants import UPPER_RIGHT
+from utilities.prefs_constants import UPPER_RIGHT
 
-from debug import print_compact_traceback ##, print_compact_stack
+from utilities.debug import print_compact_traceback ##, print_compact_stack
 
 # button region codes (must all be true values;
 # these are used as indices in various dicts or functions,
diff --git a/cad/src/graphics/behaviors/shape.py b/cad/src/graphics/behaviors/shape.py
index 007484fcf..4b80a6d68 100755
--- a/cad/src/graphics/behaviors/shape.py
+++ b/cad/src/graphics/behaviors/shape.py
@@ -35,15 +35,15 @@ from geometry.VQT import A, vlen, V
 from graphics.drawing.drawer import drawrectangle
 from graphics.drawing.drawer import drawline
 
-from constants import black
-from constants import DELETE_SELECTION
-from constants import SUBTRACT_FROM_SELECTION
-from constants import ADD_TO_SELECTION
-from constants import START_NEW_SELECTION
-from constants import white
-from constants import red
-
-from debug import print_compact_traceback
+from utilities.constants import black
+from utilities.constants import DELETE_SELECTION
+from utilities.constants import SUBTRACT_FROM_SELECTION
+from utilities.constants import ADD_TO_SELECTION
+from utilities.constants import START_NEW_SELECTION
+from utilities.constants import white
+from utilities.constants import red
+
+from utilities.debug import print_compact_traceback
 from utilities import debug_flags 
 
 from geometry.BoundingBox import BBox
diff --git a/cad/src/graphics/display_styles/CylinderChunks.py b/cad/src/graphics/display_styles/CylinderChunks.py
index 01c0c506d..ccf337a99 100755
--- a/cad/src/graphics/display_styles/CylinderChunks.py
+++ b/cad/src/graphics/display_styles/CylinderChunks.py
@@ -17,10 +17,10 @@ import foundation.env as env
 import graphics.drawing.drawer as drawer
 from geometry.geometryUtilities import matrix_putting_axis_at_z
 from geometry.VQT import V, norm
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from graphics.display_styles.displaymodes import ChunkDisplayMode
-from constants import ave_colors
-from prefs_constants import atomHighlightColor_prefs_key
+from utilities.constants import ave_colors
+from utilities.prefs_constants import atomHighlightColor_prefs_key
 
 chunkHighlightColor_prefs_key = atomHighlightColor_prefs_key # initial kluge
 
diff --git a/cad/src/graphics/display_styles/DnaCylinderChunks.py b/cad/src/graphics/display_styles/DnaCylinderChunks.py
index b22cb7d99..2b5771797 100644
--- a/cad/src/graphics/display_styles/DnaCylinderChunks.py
+++ b/cad/src/graphics/display_styles/DnaCylinderChunks.py
@@ -32,27 +32,27 @@ import foundation.env as env
 import graphics.drawing.drawer as drawer
 from geometry.geometryUtilities import matrix_putting_axis_at_z
 from geometry.VQT import V, norm, cross, angleBetween
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from graphics.display_styles.displaymodes import ChunkDisplayMode
-from constants import ave_colors, red, white, darkgreen
+from utilities.constants import ave_colors, red, white, darkgreen
 
-from prefs_constants import atomHighlightColor_prefs_key
+from utilities.prefs_constants import atomHighlightColor_prefs_key
 
 # piotr 080309: user pereferences for DNA style
-from prefs_constants import dnaStyleStrandsColor_prefs_key
-from prefs_constants import dnaStyleAxisColor_prefs_key
-from prefs_constants import dnaStyleStrutsColor_prefs_key
-from prefs_constants import dnaStyleBasesColor_prefs_key
-from prefs_constants import dnaStyleStrandsShape_prefs_key
-from prefs_constants import dnaStyleBasesShape_prefs_key
-from prefs_constants import dnaStyleStrandsArrows_prefs_key
-from prefs_constants import dnaStyleAxisShape_prefs_key
-from prefs_constants import dnaStyleStrutsShape_prefs_key
-from prefs_constants import dnaStyleStrandsScale_prefs_key
-from prefs_constants import dnaStyleAxisScale_prefs_key
-from prefs_constants import dnaStyleBasesScale_prefs_key
-from prefs_constants import dnaStyleAxisTaper_prefs_key
-from prefs_constants import dnaStyleStrutsScale_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsColor_prefs_key
+from utilities.prefs_constants import dnaStyleAxisColor_prefs_key
+from utilities.prefs_constants import dnaStyleStrutsColor_prefs_key
+from utilities.prefs_constants import dnaStyleBasesColor_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsShape_prefs_key
+from utilities.prefs_constants import dnaStyleBasesShape_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsArrows_prefs_key
+from utilities.prefs_constants import dnaStyleAxisShape_prefs_key
+from utilities.prefs_constants import dnaStyleStrutsShape_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsScale_prefs_key
+from utilities.prefs_constants import dnaStyleAxisScale_prefs_key
+from utilities.prefs_constants import dnaStyleBasesScale_prefs_key
+from utilities.prefs_constants import dnaStyleAxisTaper_prefs_key
+from utilities.prefs_constants import dnaStyleStrutsScale_prefs_key
 
 from model.elements import Singlet
 from math import sin, cos, pi
@@ -586,7 +586,7 @@ class DnaCylinderChunks(ChunkDisplayMode):
         Draws the chunk that may depend on current view.
         """
         ### drawchunk(self, glpane, chunk, selection_frame_color, memo, highlighted)
-        from constants import lightgreen
+        from utilities.constants import lightgreen
         if 0:
             if chunk.isStrandChunk(): 
                 n_bases = chunk.ladder.baselength()
diff --git a/cad/src/graphics/display_styles/SurfaceChunks.py b/cad/src/graphics/display_styles/SurfaceChunks.py
index ab1a094e8..ee34d732f 100755
--- a/cad/src/graphics/display_styles/SurfaceChunks.py
+++ b/cad/src/graphics/display_styles/SurfaceChunks.py
@@ -27,9 +27,9 @@ from geometry.VQT import V, cross
 from utilities.Log import greenmsg
 from graphics.display_styles.displaymodes import ChunkDisplayMode
 
-from constants import ave_colors
-from constants import diTrueCPK
-from prefs_constants import atomHighlightColor_prefs_key
+from utilities.constants import ave_colors
+from utilities.constants import diTrueCPK
+from utilities.prefs_constants import atomHighlightColor_prefs_key
 
 _psurface_import_worked = False
 
@@ -589,7 +589,7 @@ class SurfaceChunks(ChunkDisplayMode):
             rad = sqrt(rad)
             radius = rad + margin
             cspheres = []
-            from debug_prefs import debug_pref, Choice_boolean_True
+            from utilities.debug_prefs import debug_pref, Choice_boolean_True
             use_colors = debug_pref("surface: use colors?", Choice_boolean_True) #bruce 060927 (old code had 0 for use_colors)
             for i in range(len(spheres)):
                 st = spheres[i] / radius
diff --git a/cad/src/graphics/display_styles/displaymodes.py b/cad/src/graphics/display_styles/displaymodes.py
index 0963dcf18..490ee35c1 100755
--- a/cad/src/graphics/display_styles/displaymodes.py
+++ b/cad/src/graphics/display_styles/displaymodes.py
@@ -20,8 +20,8 @@ of our class ChunkDisplayMode. For an example, see CylinderChunks.py.
 
 # to make a new display mode for whole chunks, see the instructions in the module docstring above.
 
-import constants
-from debug import register_debug_menu_command
+import utilities.constants as constants
+from utilities.debug import register_debug_menu_command
 import foundation.env as env
 
 _display_mode_handlers = {} # maps disp_name, and also its index in constants.dispNames, to a DisplayMode instance used for drawing
@@ -55,7 +55,7 @@ class DisplayMode:
         self._hide_icon_name = getattr(self, "hide_icon_name", self._icon_name)
 
     def get_icon(self, hidden):
-        from icon_utilities import imagename_to_pixmap
+        from utilities.icon_utilities import imagename_to_pixmap
         if hidden:
             return imagename_to_pixmap( self._hide_icon_name)
         else:
diff --git a/cad/src/graphics/drawables/DirectionArrow.py b/cad/src/graphics/drawables/DirectionArrow.py
index e89cc473b..787a59367 100644
--- a/cad/src/graphics/drawables/DirectionArrow.py
+++ b/cad/src/graphics/drawables/DirectionArrow.py
@@ -27,8 +27,8 @@ from graphics.drawing.drawer import drawDirectionArrow
 
 from geometry.VQT import V, norm, vlen
 from math        import pi
-from constants   import gray, orange
-from debug       import print_compact_traceback
+from utilities.constants import gray, orange
+from utilities.debug import print_compact_traceback
 from graphics.drawables.DragHandler import DragHandler_API
 from graphics.drawables.Selobj import Selobj_API
 
diff --git a/cad/src/graphics/drawables/ResizeHandle.py b/cad/src/graphics/drawables/ResizeHandle.py
index e40949605..d42046e89 100644
--- a/cad/src/graphics/drawables/ResizeHandle.py
+++ b/cad/src/graphics/drawables/ResizeHandle.py
@@ -22,13 +22,13 @@ from OpenGL.GL import glTranslatef
 from OpenGL.GL import glRotatef
 
 from graphics.drawing.drawer import drawLineLoop, drawPlane
-from constants import black, orange, darkgreen
+from utilities.constants import black, orange, darkgreen
 
 from math import pi
 from geometry.VQT import V
 
 import foundation.env as env
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from graphics.drawables.DragHandler import DragHandler_API
 from graphics.drawables.Selobj import Selobj_API
diff --git a/cad/src/graphics/drawables/RotationHandle.py b/cad/src/graphics/drawables/RotationHandle.py
index 7f0652a93..bad754345 100644
--- a/cad/src/graphics/drawables/RotationHandle.py
+++ b/cad/src/graphics/drawables/RotationHandle.py
@@ -24,7 +24,7 @@ from exprs.ExprsConstants   import ORIGIN, DX , DY
 from exprs.dna_ribbon_view  import Cylinder
 from exprs.Rect             import Sphere
    
-from constants              import white, yellow, purple, darkgreen
+from utilities.constants import white, yellow, purple, darkgreen
 
 from geometry.VQT import V
 from exprs.DraggableHandle_AlongCircle import DraggableHandle_AlongCircle
diff --git a/cad/src/graphics/drawables/handles.py b/cad/src/graphics/drawables/handles.py
index 065e48f5e..760bf98cd 100755
--- a/cad/src/graphics/drawables/handles.py
+++ b/cad/src/graphics/drawables/handles.py
@@ -22,9 +22,9 @@ from geometry.VQT import norm
 from geometry.VQT import orthodist
 import graphics.drawing.drawer as drawer
 
-from constants import ave_colors
-from constants import magenta
-from constants import blue
+from utilities.constants import ave_colors
+from utilities.constants import magenta
+from utilities.constants import blue
 
 class handleWithHandleSet:
     """
diff --git a/cad/src/graphics/drawing/Guides.py b/cad/src/graphics/drawing/Guides.py
index c84563505..37baeaf3d 100644
--- a/cad/src/graphics/drawing/Guides.py
+++ b/cad/src/graphics/drawing/Guides.py
@@ -40,17 +40,17 @@ from PyQt4.Qt import QFont, QString, QColor
 from widgets.widget_helpers import RGBf_to_QColor
 
 from geometry.VQT import V
-from constants import  lightgray, darkgray, black
+from utilities.constants import lightgray, darkgray, black
 
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 import sys
 import foundation.env as env
-from prefs_constants import displayVertRuler_prefs_key
-from prefs_constants import displayHorzRuler_prefs_key
-from prefs_constants import rulerPosition_prefs_key
-from prefs_constants import rulerColor_prefs_key
-from prefs_constants import rulerOpacity_prefs_key
+from utilities.prefs_constants import displayVertRuler_prefs_key
+from utilities.prefs_constants import displayHorzRuler_prefs_key
+from utilities.prefs_constants import rulerPosition_prefs_key
+from utilities.prefs_constants import rulerColor_prefs_key
+from utilities.prefs_constants import rulerOpacity_prefs_key
 
 # These must match the order items appear in the ruler "Position" combobox
 # in the preferences dialog.
diff --git a/cad/src/graphics/drawing/bond_drawer.py b/cad/src/graphics/drawing/bond_drawer.py
index fee3d2a93..7e5d52cea 100755
--- a/cad/src/graphics/drawing/bond_drawer.py
+++ b/cad/src/graphics/drawing/bond_drawer.py
@@ -37,28 +37,28 @@ from graphics.rendering.povray.povheader import povpoint
 from utilities.Printing import Vector3ToString
 from model.elements import Singlet
 
-from debug import print_compact_stack, print_compact_traceback
-
-from constants import diDEFAULT
-from constants import diINVISIBLE
-from constants import diLINES
-from constants import diBALL
-from constants import diTUBES
-from constants import diTrueCPK
-from constants import diDNACYLINDER
-
-from constants import TubeRadius
-from constants import diBALL_SigmaBondRadius
-from constants import diDNACYLINDER_SigmaBondRadius
-
-from constants import ave_colors
-from constants import green
-from constants import yellow
-from constants import red
-from constants import blue
-from constants import black
-from constants import white
-from constants import orange
+from utilities.debug import print_compact_stack, print_compact_traceback
+
+from utilities.constants import diDEFAULT
+from utilities.constants import diINVISIBLE
+from utilities.constants import diLINES
+from utilities.constants import diBALL
+from utilities.constants import diTUBES
+from utilities.constants import diTrueCPK
+from utilities.constants import diDNACYLINDER
+
+from utilities.constants import TubeRadius
+from utilities.constants import diBALL_SigmaBondRadius
+from utilities.constants import diDNACYLINDER_SigmaBondRadius
+
+from utilities.constants import ave_colors
+from utilities.constants import green
+from utilities.constants import yellow
+from utilities.constants import red
+from utilities.constants import blue
+from utilities.constants import black
+from utilities.constants import white
+from utilities.constants import orange
 
 from model.bond_constants import V_SINGLE
 from model.bond_constants import V_DOUBLE
@@ -68,21 +68,21 @@ from model.bond_constants import V_AROMATIC
 from model.bond_constants import V_GRAPHITE
 from model.bond_constants import V_CARBOMERIC
 
-from prefs_constants import _default_toolong_hicolor ## not yet in prefs db?
-from prefs_constants import diBALL_BondCylinderRadius_prefs_key
-from prefs_constants import diDNACYLINDER_BondCylinderRadius_prefs_key
-from prefs_constants import pibondLetters_prefs_key
-from prefs_constants import pibondStyle_prefs_key
-from prefs_constants import arrowsOnFivePrimeEnds_prefs_key
-from prefs_constants import arrowsOnThreePrimeEnds_prefs_key
-from prefs_constants import arrowsOnBackBones_prefs_key
-from prefs_constants import showBondStretchIndicators_prefs_key
-from prefs_constants import linesDisplayModeThickness_prefs_key
-from prefs_constants import bondStretchColor_prefs_key
-from prefs_constants import diBALL_bondcolor_prefs_key
-from prefs_constants import dnaStrutScaleFactor_prefs_key
-
-from GlobalPreferences import disable_do_not_draw_open_bonds
+from utilities.prefs_constants import _default_toolong_hicolor ## not yet in prefs db?
+from utilities.prefs_constants import diBALL_BondCylinderRadius_prefs_key
+from utilities.prefs_constants import diDNACYLINDER_BondCylinderRadius_prefs_key
+from utilities.prefs_constants import pibondLetters_prefs_key
+from utilities.prefs_constants import pibondStyle_prefs_key
+from utilities.prefs_constants import arrowsOnFivePrimeEnds_prefs_key
+from utilities.prefs_constants import arrowsOnThreePrimeEnds_prefs_key
+from utilities.prefs_constants import arrowsOnBackBones_prefs_key
+from utilities.prefs_constants import showBondStretchIndicators_prefs_key
+from utilities.prefs_constants import linesDisplayModeThickness_prefs_key
+from utilities.prefs_constants import bondStretchColor_prefs_key
+from utilities.prefs_constants import diBALL_bondcolor_prefs_key
+from utilities.prefs_constants import dnaStrutScaleFactor_prefs_key
+
+from utilities.GlobalPreferences import disable_do_not_draw_open_bonds
 
 # ==
 
@@ -523,7 +523,7 @@ def draw_bond_main( self, glpane, disp, col, level, highlighted, povfile = None,
     if self.v6 != V_SINGLE:
         if draw_vanes:
             if debug_flags.atom_debug:
-                import graphics.drawing.draw_bond_vanes as draw_bond_vanes, debug
+                import graphics.drawing.draw_bond_vanes as draw_bond_vanes, utilities.debug as debug
                 debug.reload_once_per_event(draw_bond_vanes) #bruce 050825 renabled this, using reload_once_per_event
             from graphics.drawing.draw_bond_vanes import draw_bond_vanes
             draw_bond_vanes( self, glpane, sigmabond_cyl_radius, col) # this calls self.get_pi_info()
diff --git a/cad/src/graphics/drawing/drawDnaRibbons.py b/cad/src/graphics/drawing/drawDnaRibbons.py
index b65b7f8f5..6711eac9e 100755
--- a/cad/src/graphics/drawing/drawDnaRibbons.py
+++ b/cad/src/graphics/drawing/drawDnaRibbons.py
@@ -32,8 +32,8 @@ from graphics.drawing.drawer import drawPoint
 from graphics.drawing.drawer import drawsphere
 
 from geometry.VQT import norm, vlen, V, cross
-from constants import white
-from constants import diBALL, diTrueCPK, diTUBES, diLINES
+from utilities.constants import white
+from utilities.constants import diBALL, diTrueCPK, diTUBES, diLINES
 
 
 #Constants for drawing the ribbon points as spheres.
diff --git a/cad/src/graphics/drawing/draw_bond_vanes.py b/cad/src/graphics/drawing/draw_bond_vanes.py
index e7726c909..1665a0a22 100755
--- a/cad/src/graphics/drawing/draw_bond_vanes.py
+++ b/cad/src/graphics/drawing/draw_bond_vanes.py
@@ -34,8 +34,8 @@ from geometry.VQT import cross, vlen, norm
 import foundation.env as env
 import graphics.drawing.drawer as drawer
 
-from constants import white
-from prefs_constants import pibondStyle_prefs_key
+from utilities.constants import white
+from utilities.prefs_constants import pibondStyle_prefs_key
 
 MAXTWIST = 5 * math.pi / 180 # permissible twist of one vane segment (5 degrees -- just a guess)
 
@@ -68,7 +68,7 @@ def draw_vane( bond, a1p, a2p, ord_pi, rad, col ):
     If col is not boolean false, use it as the vane color; otherwise, use a constant color
     which might be influenced by the pi orbital occupancy.
     """
-    from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
     ## twisted = debug_pref('pi vanes/ribbons', Choice_boolean_False)
     pi_bond_style = env.prefs[ pibondStyle_prefs_key] # one of ['multicyl','vane','ribbon']
     twisted = (pi_bond_style == 'ribbon')
@@ -99,7 +99,7 @@ def draw_vane( bond, a1p, a2p, ord_pi, rad, col ):
         #bruce 050804: initial test of bond color prefs; inadequate in several ways #######@@@@@@@
         from foundation.preferences import prefs_context
         prefs = prefs_context()
-        from prefs_constants import bondVaneColor_prefs_key
+        from utilities.prefs_constants import bondVaneColor_prefs_key
         color = prefs.get(bondVaneColor_prefs_key) #k I hope this color tuple of floats is in the correct prefs format
         assert len(color) == 3 # protect following code from color being None (which causes bus error, maybe in PyOpenGL)
         
diff --git a/cad/src/graphics/drawing/draw_grid_lines.py b/cad/src/graphics/drawing/draw_grid_lines.py
index 0fe87b2f8..60b7de0d9 100644
--- a/cad/src/graphics/drawing/draw_grid_lines.py
+++ b/cad/src/graphics/drawing/draw_grid_lines.py
@@ -129,7 +129,7 @@ def drawGPGrid(glpane, color, line_type, w, h, uw, uh, up, right):
     uw = width spacing between grid lines
     uh = height spacing between grid lines
     """
-    from prefs_constants import NO_LINE, SOLID_LINE, DASHED_LINE, DOTTED_LINE
+    from utilities.prefs_constants import NO_LINE, SOLID_LINE, DASHED_LINE, DOTTED_LINE
     
     if line_type == NO_LINE:
         return
@@ -229,7 +229,7 @@ def drawSiCGrid(color, line_type, w, h, up, right):
     """
     Draw SiC grid.
     """
-    from prefs_constants import NO_LINE, SOLID_LINE, DASHED_LINE, DOTTED_LINE
+    from utilities.prefs_constants import NO_LINE, SOLID_LINE, DASHED_LINE, DOTTED_LINE
     
     if line_type == NO_LINE:
         return
diff --git a/cad/src/graphics/drawing/drawer.py b/cad/src/graphics/drawing/drawer.py
index 541ae8e56..8208838a6 100755
--- a/cad/src/graphics/drawing/drawer.py
+++ b/cad/src/graphics/drawing/drawer.py
@@ -196,21 +196,21 @@ except:
 from geometry.VQT import norm, vlen, V, Q, A
 import foundation.env as env #bruce 051126
 
-from constants import white, blue, red
-from constants import darkgreen, lightblue
-from constants import DIAMOND_BOND_LENGTH
-from prefs_constants import material_specular_highlights_prefs_key
-from prefs_constants import material_specular_shininess_prefs_key
-from prefs_constants import material_specular_finish_prefs_key
-from prefs_constants import material_specular_brightness_prefs_key
+from utilities.constants import white, blue, red
+from utilities.constants import darkgreen, lightblue
+from utilities.constants import DIAMOND_BOND_LENGTH
+from utilities.prefs_constants import material_specular_highlights_prefs_key
+from utilities.prefs_constants import material_specular_shininess_prefs_key
+from utilities.prefs_constants import material_specular_finish_prefs_key
+from utilities.prefs_constants import material_specular_brightness_prefs_key
 
-import debug # for debug.print_compact_traceback
+import utilities.debug as debug # for debug.print_compact_traceback
 
 # this can't be done at toplevel due to a recursive import issue.
 # TODO: fix by splitting this module (drawer) into smaller files.
 ## from Font3D import Font3D
 
-import EndUser
+import utilities.EndUser as EndUser
 
 # ==
 
@@ -911,7 +911,7 @@ def get_gl_info_string(glpane): # grantham 20051129
     gl_info_string += 'GL_RENDERER : "%s"\n' % glGetString(GL_RENDERER)
     gl_info_string += 'GL_EXTENSIONS : "%s"\n' % glGetString(GL_EXTENSIONS)
 
-    from debug_prefs import debug_pref, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_False
     if debug_pref("get_gl_info_string call glAreTexturesResident?", Choice_boolean_False):
         # Give a practical indication of how much video memory is available.
         # Should also do this with VBOs.
@@ -974,7 +974,7 @@ def drawwiresphere_worker(params):
 
     (color, pos, radius, detailLevel) = params
     ## assert detailLevel == 1 # true, but leave out for speed
-    from debug_prefs import debug_pref, Choice_boolean_True
+    from utilities.debug_prefs import debug_pref, Choice_boolean_True
     newway = debug_pref("new wirespheres?", Choice_boolean_True) #bruce 060415 experiment, re iMac G4 wiresphere bug; fixes it!
     oldway = not newway
     # These objects want a constant line color even if they are selected or highlighted.
@@ -1794,7 +1794,7 @@ class ColorSorter:
         Finish sorting - objects recorded since "start" will
         be sorted and invoked now.
         """
-        from debug_prefs import debug_pref, Choice_boolean_False
+        from utilities.debug_prefs import debug_pref, Choice_boolean_False
         debug_which_renderer = debug_pref("debug print which renderer", Choice_boolean_False) #bruce 060314, imperfect but tolerable
 
         parent_csdl = ColorSorter.parent_csdl
@@ -2181,8 +2181,8 @@ def setup_drawer():
     glEndList()
 
     # Debug Preferences
-    from debug_prefs import debug_pref, Choice_boolean_True
-    from debug_prefs import Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_True
+    from utilities.debug_prefs import Choice_boolean_False
     choices = [Choice_boolean_False, Choice_boolean_True]
 
     # 20060314 grantham
@@ -3179,7 +3179,7 @@ def drawFullWindow(vtColors):
        left-down, right-down, right-up, left-up window corners.
        To draw the full window, the modelview and projection should be set in identity.
        """
-    from constants import GL_FAR_Z
+    from utilities.constants import GL_FAR_Z
     glDisable(GL_LIGHTING)
 
     glBegin(GL_QUADS)
@@ -3290,7 +3290,7 @@ def renderSurface(surfaceEntities, surfaceNormals):
     nc = len(surfaceColors)
     if 1:
         ### bruce 060927 debug code; when done debugging, we can change them to constants & simplify the code that uses them.
-        from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+        from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
         disable_lighting = debug_pref("surface: disable lighting?", Choice_boolean_False)
         if nc:
             color_first = debug_pref("surface: color before vertex?", Choice_boolean_True)
diff --git a/cad/src/graphics/drawing/texture_fonts.py b/cad/src/graphics/drawing/texture_fonts.py
index 94d9bb231..b36eacdcb 100644
--- a/cad/src/graphics/drawing/texture_fonts.py
+++ b/cad/src/graphics/drawing/texture_fonts.py
@@ -18,7 +18,7 @@ from OpenGL.GLU import gluUnProject
 
 import foundation.env as env
 
-from icon_utilities import image_directory # for finding texture files
+from utilities.icon_utilities import image_directory # for finding texture files
 
 from geometry.VQT import V, A, vlen
 
diff --git a/cad/src/graphics/drawing/texture_helpers.py b/cad/src/graphics/drawing/texture_helpers.py
index 7aaddf1f0..c89582f78 100644
--- a/cad/src/graphics/drawing/texture_helpers.py
+++ b/cad/src/graphics/drawing/texture_helpers.py
@@ -32,8 +32,8 @@ from OpenGL.GL import glTexEnvf
 
 from OpenGL.GLU import gluBuild2DMipmaps
 
-from debug_prefs import Choice_boolean_False   # in disabled code
-from debug_prefs import debug_pref   # in disabled code
+from utilities.debug_prefs import Choice_boolean_False   # in disabled code
+from utilities.debug_prefs import debug_pref   # in disabled code
 
 # note this runtime import below -- TODO, find out if it can be toplevel;
 # the file it imports is not now [071017] in any import cycles:
diff --git a/cad/src/graphics/images/ImageUtils.py b/cad/src/graphics/images/ImageUtils.py
index e4835c265..6289010ba 100755
--- a/cad/src/graphics/images/ImageUtils.py
+++ b/cad/src/graphics/images/ImageUtils.py
@@ -24,7 +24,7 @@ import PngImagePlugin # Don't remove this, it is used by package creator to find
 PngImagePlugin
 
 from utilities import debug_flags #bruce 061127
-from debug import print_compact_traceback #bruce 061128
+from utilities.debug import print_compact_traceback #bruce 061128
 
 class nEImageOps:
     """
@@ -107,7 +107,7 @@ class nEImageOps:
             print "debug fyi: nEImageOps.__init__: %r.img.size, mode is %r, %r" % (self, self.img.size, self.img.mode) ###
         if 1:
             #bruce 060213 - let debug pref set default values of ideal_width, ideal_height
-            from debug_prefs import debug_pref, Choice
+            from utilities.debug_prefs import debug_pref, Choice
             self.ideal_width = self.ideal_height = debug_pref("image size", Choice([256,128,64,32,512,1024]),
                 prefs_key = 'A8 devel/image size' ) #bruce 060612 made this persistent
             # these are not used until client code calls getTextureData;
@@ -263,7 +263,7 @@ class nEImageOps:
         #  work before or after image is loaded. The docs mentioned elsewhere
         #  are not very clear about this.] 
         import os
-        from PlatformDependent import find_or_make_Nanorex_subdir
+        from platform.PlatformDependent import find_or_make_Nanorex_subdir
         nhdir = find_or_make_Nanorex_subdir("Nano-Hive")
         basename = os.path.basename(self.imageName)
         if self._tmpmode:
diff --git a/cad/src/graphics/rendering/fileIO.py b/cad/src/graphics/rendering/fileIO.py
index ff9c5d88e..cd97e3daf 100755
--- a/cad/src/graphics/rendering/fileIO.py
+++ b/cad/src/graphics/rendering/fileIO.py
@@ -25,10 +25,10 @@ from graphics.rendering.povray.povheader import povheader, povpoint
 from graphics.rendering.mdl.mdldata import mdlheader
 from graphics.rendering.mdl.mdldata import mdlfooter
 
-from constants import diINVISIBLE
-from prefs_constants import PERSPECTIVE
-from prefs_constants import material_specular_highlights_prefs_key
-from prefs_constants import material_specular_finish_prefs_key
+from utilities.constants import diINVISIBLE
+from utilities.prefs_constants import PERSPECTIVE
+from utilities.prefs_constants import material_specular_highlights_prefs_key
+from utilities.prefs_constants import material_specular_finish_prefs_key
 
 # ==
 
diff --git a/cad/src/graphics/rendering/povray/povray.py b/cad/src/graphics/rendering/povray/povray.py
index 5cf900b03..ed5971032 100755
--- a/cad/src/graphics/rendering/povray/povray.py
+++ b/cad/src/graphics/rendering/povray/povray.py
@@ -24,14 +24,14 @@ from PyQt4.Qt import QApplication, QCursor, Qt, QStringList, QProcess, QMessageB
 
 import foundation.env as env
 from utilities.Log import orangemsg ##, redmsg, greenmsg, _graymsg
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from prefs_constants import megapov_enabled_prefs_key
-from prefs_constants import megapov_path_prefs_key
-from prefs_constants import povray_enabled_prefs_key
-from prefs_constants import povray_path_prefs_key
-from prefs_constants import povdir_enabled_prefs_key
-from prefs_constants import povdir_path_prefs_key
+from utilities.prefs_constants import megapov_enabled_prefs_key
+from utilities.prefs_constants import megapov_path_prefs_key
+from utilities.prefs_constants import povray_enabled_prefs_key
+from utilities.prefs_constants import povray_path_prefs_key
+from utilities.prefs_constants import povdir_enabled_prefs_key
+from utilities.prefs_constants import povdir_path_prefs_key
 
 def _dialog_to_offer_prefs_fixup(win, caption, text, macwarning_ok): #bruce 060710 [use Plugin.py instead?]
     """
@@ -311,7 +311,7 @@ def launch_povray_or_megapov(win, info, povray_ini): #bruce 060707/11 revised th
             if arg != "":
                 arguments.append(arg)
 
-        from Process import Process
+        from processes.Process import Process
         p = Process()
             #bruce 060707: this doesn't take advantage of anything not in QProcess,
             # unless it matters that it reads and discards stdout/stderr
diff --git a/cad/src/graphics/rendering/qutemol/qutemol.py b/cad/src/graphics/rendering/qutemol/qutemol.py
index 112c667a4..88191fa88 100755
--- a/cad/src/graphics/rendering/qutemol/qutemol.py
+++ b/cad/src/graphics/rendering/qutemol/qutemol.py
@@ -25,24 +25,24 @@ import os
 import sys
 from PyQt4.Qt import QString, QStringList, QProcess
 
-from prefs_constants import qutemol_enabled_prefs_key, qutemol_path_prefs_key
-from debug import print_compact_traceback
-from debug_prefs import debug_pref, Choice_boolean_True
-from constants import properDisplayNames, TubeRadius, diBALL_SigmaBondRadius
+from utilities.prefs_constants import qutemol_enabled_prefs_key, qutemol_path_prefs_key
+from utilities.debug import print_compact_traceback
+from utilities.debug_prefs import debug_pref, Choice_boolean_True
+from utilities.constants import properDisplayNames, TubeRadius, diBALL_SigmaBondRadius
 from files.pdb.files_pdb import writePDB_Header, writepdb, EXCLUDE_HIDDEN_ATOMS
 from model.elements import PeriodicTable
 
-from prefs_constants import cpkScaleFactor_prefs_key
-from prefs_constants import diBALL_AtomRadius_prefs_key
-from prefs_constants import backgroundGradient_prefs_key
-from prefs_constants import backgroundColor_prefs_key
-from prefs_constants import diBALL_BondCylinderRadius_prefs_key
+from utilities.prefs_constants import cpkScaleFactor_prefs_key
+from utilities.prefs_constants import diBALL_AtomRadius_prefs_key
+from utilities.prefs_constants import backgroundGradient_prefs_key
+from utilities.prefs_constants import backgroundColor_prefs_key
+from utilities.prefs_constants import diBALL_BondCylinderRadius_prefs_key
 
-from Plugins import checkPluginPreferences
+from processes.Plugins import checkPluginPreferences
 
-from Process import Process
+from processes.Process import Process
 from commands.GroupProperties.GroupProp import Statistics
-from PlatformDependent import find_or_make_Nanorex_subdir
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
 
 def launch_qutemol(pdb_file):
     """
diff --git a/cad/src/graphics/widgets/DynamicTip.py b/cad/src/graphics/widgets/DynamicTip.py
index a34765a16..6581dc082 100755
--- a/cad/src/graphics/widgets/DynamicTip.py
+++ b/cad/src/graphics/widgets/DynamicTip.py
@@ -42,19 +42,19 @@ from model.jigs import Jig
 from geometry.VQT import vlen
 from geometry.VQT import atom_angle_radians
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
-from prefs_constants import dynamicToolTipWakeUpDelay_prefs_key
-from prefs_constants import dynamicToolTipAtomDistancePrecision_prefs_key
-from prefs_constants import dynamicToolTipBendAnglePrecision_prefs_key
-from prefs_constants import dynamicToolTipTorsionAnglePrecision_prefs_key
-from prefs_constants import dynamicToolTipAtomChunkInfo_prefs_key
-from prefs_constants import dynamicToolTipBondChunkInfo_prefs_key
-from prefs_constants import dynamicToolTipAtomPosition_prefs_key
-from prefs_constants import dynamicToolTipAtomDistanceDeltas_prefs_key
-from prefs_constants import dynamicToolTipBondLength_prefs_key
-from prefs_constants import dynamicToolTipAtomMass_prefs_key
-from prefs_constants import dynamicToolTipVdwRadiiInAtomDistance_prefs_key
+from utilities.prefs_constants import dynamicToolTipWakeUpDelay_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomDistancePrecision_prefs_key
+from utilities.prefs_constants import dynamicToolTipBendAnglePrecision_prefs_key
+from utilities.prefs_constants import dynamicToolTipTorsionAnglePrecision_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomChunkInfo_prefs_key
+from utilities.prefs_constants import dynamicToolTipBondChunkInfo_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomPosition_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomDistanceDeltas_prefs_key
+from utilities.prefs_constants import dynamicToolTipBondLength_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomMass_prefs_key
+from utilities.prefs_constants import dynamicToolTipVdwRadiiInAtomDistance_prefs_key
 
 class DynamicTip: # Mark and Ninad 060817.
     """
diff --git a/cad/src/graphics/widgets/GLPane.py b/cad/src/graphics/widgets/GLPane.py
index 69251bc87..87315c574 100755
--- a/cad/src/graphics/widgets/GLPane.py
+++ b/cad/src/graphics/widgets/GLPane.py
@@ -132,11 +132,11 @@ from commandSequencer.CommandSequencer import modeMixin
 from utilities import debug_flags
 
 from utilities.Log import orangemsg
-from PlatformDependent import fix_event_helper
-from PlatformDependent import wrap_key_event
-from menu_helpers import makemenu_helper
-from DebugMenuMixin import DebugMenuMixin
-from debug import print_compact_traceback, print_compact_stack
+from platform.PlatformDependent import fix_event_helper
+from platform.PlatformDependent import wrap_key_event
+from widgets.menu_helpers import makemenu_helper
+from widgets.DebugMenuMixin import DebugMenuMixin
+from utilities.debug import print_compact_traceback, print_compact_stack
 import foundation.preferences as preferences
 import foundation.env as env
 from foundation.changes import SubUsageTrackingMixin
@@ -147,43 +147,43 @@ from graphics.drawing.Guides import Guides
 
 from foundation.state_utils import transclose
 
-from prefs_constants import glpane_lights_prefs_key
-from prefs_constants import compassPosition_prefs_key
-from prefs_constants import defaultProjection_prefs_key
-from prefs_constants import defaultDisplayMode_prefs_key
-from prefs_constants import backgroundColor_prefs_key
-from prefs_constants import backgroundGradient_prefs_key
-from prefs_constants import animateStandardViews_prefs_key
-from prefs_constants import animateMaximumTime_prefs_key
-from prefs_constants import light1Color_prefs_key
-from prefs_constants import light2Color_prefs_key
-from prefs_constants import light3Color_prefs_key
-from prefs_constants import displayCompass_prefs_key
-from prefs_constants import displayOriginAxis_prefs_key
-from prefs_constants import displayOriginAsSmallAxis_prefs_key
-from prefs_constants import UPPER_RIGHT
-from prefs_constants import UPPER_LEFT
-from prefs_constants import LOWER_LEFT
-from prefs_constants import displayCompassLabels_prefs_key
-from prefs_constants import displayRulers_prefs_key
-from prefs_constants import showRulersInPerspectiveView_prefs_key
-
-from constants import diDEFAULT
-from constants import dispLabel
-from constants import GL_FAR_Z
-from constants import bluesky
-from constants import white
-from constants import MULTIPANE_GUI
-
-from debug_prefs import Choice
-from debug_prefs import Choice_boolean_False
-from debug_prefs import debug_pref
-
-from GlobalPreferences import DEBUG_BAREMOTION
+from utilities.prefs_constants import glpane_lights_prefs_key
+from utilities.prefs_constants import compassPosition_prefs_key
+from utilities.prefs_constants import defaultProjection_prefs_key
+from utilities.prefs_constants import defaultDisplayMode_prefs_key
+from utilities.prefs_constants import backgroundColor_prefs_key
+from utilities.prefs_constants import backgroundGradient_prefs_key
+from utilities.prefs_constants import animateStandardViews_prefs_key
+from utilities.prefs_constants import animateMaximumTime_prefs_key
+from utilities.prefs_constants import light1Color_prefs_key
+from utilities.prefs_constants import light2Color_prefs_key
+from utilities.prefs_constants import light3Color_prefs_key
+from utilities.prefs_constants import displayCompass_prefs_key
+from utilities.prefs_constants import displayOriginAxis_prefs_key
+from utilities.prefs_constants import displayOriginAsSmallAxis_prefs_key
+from utilities.prefs_constants import UPPER_RIGHT
+from utilities.prefs_constants import UPPER_LEFT
+from utilities.prefs_constants import LOWER_LEFT
+from utilities.prefs_constants import displayCompassLabels_prefs_key
+from utilities.prefs_constants import displayRulers_prefs_key
+from utilities.prefs_constants import showRulersInPerspectiveView_prefs_key
+
+from utilities.constants import diDEFAULT
+from utilities.constants import dispLabel
+from utilities.constants import GL_FAR_Z
+from utilities.constants import bluesky
+from utilities.constants import white
+from utilities.constants import MULTIPANE_GUI
+
+from utilities.debug_prefs import Choice
+from utilities.debug_prefs import Choice_boolean_False
+from utilities.debug_prefs import debug_pref
+
+from utilities.GlobalPreferences import DEBUG_BAREMOTION
 
 from graphics.widgets.GLPane_minimal import GLPane_minimal
 
-import qt4transition
+import utilities.qt4transition as qt4transition
 
 # suspicious imports [should not really be needed, according to bruce 070919]
 from model.bonds import Bond # used only for selobj ordering
@@ -3168,7 +3168,7 @@ class GLPane(GLPane_minimal, modeMixin, DebugMenuMixin, SubUsageTrackingMixin,
 
         # draw some test images related to the confirmation corner
 
-        from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+        from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
 
         ccdp1 = debug_pref("Conf corner test: redraw at lower left", Choice_boolean_False, prefs_key = True)
         ccdp2 = debug_pref("Conf corner test: redraw in-place", Choice_boolean_False, prefs_key = True) # default changed, same prefs_key
diff --git a/cad/src/graphics/widgets/GLPane_minimal.py b/cad/src/graphics/widgets/GLPane_minimal.py
index 0ad45b983..373b21607 100644
--- a/cad/src/graphics/widgets/GLPane_minimal.py
+++ b/cad/src/graphics/widgets/GLPane_minimal.py
@@ -21,12 +21,12 @@ from geometry.VQT import V, Q
 from graphics.behaviors.Trackball import Trackball
 from model.NamedView import NamedView
 
-from prefs_constants import undoRestoreView_prefs_key
+from utilities.prefs_constants import undoRestoreView_prefs_key
 
-from debug_prefs import Choice
-from debug_prefs import debug_pref
+from utilities.debug_prefs import Choice
+from utilities.debug_prefs import debug_pref
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 import foundation.env as env
 
diff --git a/cad/src/graphics/widgets/ThumbView.py b/cad/src/graphics/widgets/ThumbView.py
index e2c7a771e..9a481d307 100755
--- a/cad/src/graphics/widgets/ThumbView.py
+++ b/cad/src/graphics/widgets/ThumbView.py
@@ -70,20 +70,20 @@ import foundation.env as env
 from utilities import debug_flags
 
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from constants import diTrueCPK
-from constants import gray
-from constants import bluesky
-from constants import GL_FAR_Z
-from prefs_constants import bondpointHighlightColor_prefs_key
+from utilities.constants import diTrueCPK
+from utilities.constants import gray
+from utilities.constants import bluesky
+from utilities.constants import GL_FAR_Z
+from utilities.prefs_constants import bondpointHighlightColor_prefs_key
 
 from foundation.Group import Group
 from model.chem import Atom
 from model.elements import Singlet
 from model.chunk import Chunk
 
-from pastables import find_hotspot_for_pasting
+from operations.pastables import find_hotspot_for_pasting
 
 from graphics.widgets.GLPane_minimal import GLPane_minimal
 
@@ -324,7 +324,7 @@ class ThumbView(GLPane_minimal):
         self.setDepthRange_setup_from_debug_pref()
         self.setDepthRange_Normal()
         
-        from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+        from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
         if debug_pref("always setup_lighting?", Choice_boolean_False):
             #bruce 060415 added debug_pref("always setup_lighting?"), in GLPane and ThumbView [KEEP DFLTS THE SAME!!];
             # see comments in GLPane
diff --git a/cad/src/history/HistoryWidget.py b/cad/src/history/HistoryWidget.py
index 80472a81f..bab11123d 100755
--- a/cad/src/history/HistoryWidget.py
+++ b/cad/src/history/HistoryWidget.py
@@ -31,17 +31,17 @@ from PyQt4.Qt import Qt
 from PyQt4.Qt import QTextEdit, QTextOption
 
 from utilities import debug_flags
-from PlatformDependent import mkdirs_in_filename
-from DebugMenuMixin import DebugMenuMixin
+from platform.PlatformDependent import mkdirs_in_filename
+from widgets.DebugMenuMixin import DebugMenuMixin
 import foundation.env as env
 
-from prefs_constants import historyMsgTimestamp_prefs_key
-from prefs_constants import historyMsgSerialNumber_prefs_key
-from prefs_constants import historyHeight_prefs_key
+from utilities.prefs_constants import historyMsgTimestamp_prefs_key
+from utilities.prefs_constants import historyMsgSerialNumber_prefs_key
+from utilities.prefs_constants import historyHeight_prefs_key
 
 from utilities.Log import graymsg, quote_html, greenmsg, redmsg, orangemsg
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
 class message:
     """
@@ -428,9 +428,9 @@ class HistoryWidget:
         if not msg:
             return
         # now handle the present msg: save (and show transiently) or emit
-        from debug_prefs import debug_pref, Choice_boolean_False
+        from utilities.debug_prefs import debug_pref, Choice_boolean_False
         if debug_pref("print history.message() call stacks?", Choice_boolean_False): #bruce 060720
-            from debug import compact_stack
+            from utilities.debug import compact_stack
             options['compact_stack'] = compact_stack(skip_innermost_n = 2) # skips compact_stack itself, and this line that calls it
         if transient_id:
             self.statusbar_msg(msg, repaint = repaint) # (no html allowed in msg!)
diff --git a/cad/src/main.py b/cad/src/main.py
index b5712e1c6..63ac22df3 100755
--- a/cad/src/main.py
+++ b/cad/src/main.py
@@ -121,7 +121,7 @@ def _start_NE1():
     # NOTE: imports of NE1 source modules MUST NOT BE DONE until after the
     # optional sys.path change done for _alternateSourcePath, just above.
 
-    import EndUser
+    import utilities.EndUser as EndUser
 
     EndUser.setAlternateSourcePath(_alternateSourcePath)
     
diff --git a/cad/src/model/Comment.py b/cad/src/model/Comment.py
index 5d925c32d..a4dce62c4 100755
--- a/cad/src/model/Comment.py
+++ b/cad/src/model/Comment.py
@@ -14,8 +14,8 @@ registering it with files_mmp_registration instead of hardcoding it there
 """
 
 from foundation.Utility import SimpleCopyMixin, Node
-from icon_utilities import imagename_to_pixmap
-from constants import gensym
+from utilities.icon_utilities import imagename_to_pixmap
+from utilities.constants import gensym
 
 from files.mmp.files_mmp_registration import MMP_RecordParser
 from files.mmp.files_mmp_registration import register_MMP_RecordParser
diff --git a/cad/src/model/Line.py b/cad/src/model/Line.py
index 4c23278b4..45b91aaab 100755
--- a/cad/src/model/Line.py
+++ b/cad/src/model/Line.py
@@ -20,8 +20,8 @@ from Numeric    import dot
 from math       import pi, cos
 from geometry.VQT import V, Q, cross, A, planeXline, vlen, norm, angleBetween
 
-from debug     import print_compact_traceback
-from constants import blue
+from utilities.debug import print_compact_traceback
+from utilities.constants import blue
 from graphics.drawables.ResizeHandle import ResizeHandle
 from model.ReferenceGeometry import ReferenceGeometry
 
diff --git a/cad/src/model/NamedView.py b/cad/src/model/NamedView.py
index fc1fba58c..21a5e9dee 100644
--- a/cad/src/model/NamedView.py
+++ b/cad/src/model/NamedView.py
@@ -17,9 +17,9 @@ Mark renamed Csys to NamedView, on or after 2008-02-03.
 Bruce 080303 simplified NamedView.__init__ arg signature and some calling code.
 """
 
-from constants import gensym
+from utilities.constants import gensym
 from geometry.VQT import V, Q, vlen
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 from foundation.Utility import SimpleCopyMixin
 from foundation.Utility import Node
 from utilities import debug_flags
diff --git a/cad/src/model/Plane.py b/cad/src/model/Plane.py
index 0daf13caa..cff5de1be 100755
--- a/cad/src/model/Plane.py
+++ b/cad/src/model/Plane.py
@@ -25,12 +25,12 @@ from OpenGL.GL import glTranslatef
 from OpenGL.GL import glRotatef
 
 from graphics.drawing.drawer import drawLineLoop, drawPlane
-from constants  import black, orange, yellow, darkgreen, brown
+from utilities.constants import black, orange, yellow, darkgreen, brown
 
 from geometry.VQT import V, Q, cross, planeXline, vlen, norm, ptonline
 from geometry.BoundingBox import BBox
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 import foundation.env as env
 
 from utilities.Log     import redmsg
diff --git a/cad/src/model/PovrayScene.py b/cad/src/model/PovrayScene.py
index 69713936c..856056368 100755
--- a/cad/src/model/PovrayScene.py
+++ b/cad/src/model/PovrayScene.py
@@ -21,13 +21,13 @@ from PyQt4.Qt import QApplication
 
 import foundation.env as env
 from foundation.Utility import SimpleCopyMixin, Node
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 from graphics.rendering.povray.povray import decode_povray_prefs, write_povray_ini_file, launch_povray_or_megapov
 from graphics.rendering.fileIO import writepovfile
 from utilities.Log import redmsg, orangemsg, greenmsg, _graymsg
 from utilities import debug_flags
-from PlatformDependent import find_or_make_Nanorex_subdir
-from debug import print_compact_traceback
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
+from utilities.debug import print_compact_traceback
 
 import re
 from files.mmp.files_mmp_registration import MMP_RecordParser
diff --git a/cad/src/model/ReferenceGeometry.py b/cad/src/model/ReferenceGeometry.py
index 5009f7ead..1f28204da 100755
--- a/cad/src/model/ReferenceGeometry.py
+++ b/cad/src/model/ReferenceGeometry.py
@@ -29,9 +29,9 @@ some methods in this file have become overdefined. This needs cleanup
 import foundation.env as env
 from utilities import debug_flags
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from constants import darkgreen, orange, yellow
+from utilities.constants import darkgreen, orange, yellow
 
 from OpenGL.GL import glPushName
 from OpenGL.GL import glPopName
diff --git a/cad/src/model/assembly.py b/cad/src/model/assembly.py
index 5b3c60d77..7975d153c 100755
--- a/cad/src/model/assembly.py
+++ b/cad/src/model/assembly.py
@@ -67,24 +67,24 @@ on __xxx__ attrs in python objects.
 import os
 import time
 
-import Initialize
+import utilities.Initialize as Initialize
 
 from foundation.Utility import node_name
 from foundation.Group import Group
-from pastables import is_pastable
+from operations.pastables import is_pastable
 
-from debug import print_compact_traceback
-from prefs_constants import workingDirectory_prefs_key
+from utilities.debug import print_compact_traceback
+from utilities.prefs_constants import workingDirectory_prefs_key
 
 from utilities.Log import orangemsg ##, greenmsg, redmsg
 from utilities import debug_flags
-from PlatformDependent import find_or_make_any_directory
+from platform.PlatformDependent import find_or_make_any_directory
 import foundation.env as env
 from foundation.state_utils import StateMixin, IdentityCopyMixin
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 import foundation.undo_archive as undo_archive
 
-from constants import gensym, SELWHAT_CHUNKS, SELWHAT_ATOMS
+from utilities.constants import gensym, SELWHAT_CHUNKS, SELWHAT_ATOMS
 from foundation.state_constants import S_CHILD, S_DATA, S_REF
 
 from model.part import Part as Part_class # use a name we can search for [bruce 071029]
@@ -93,7 +93,7 @@ from model.part import Part as Part_class # use a name we can search for [bruce
 from model.part import MainPart
 from model.part import ClipboardItemPart
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 from commands.PartProperties.PartProp import PartProp
 from PyQt4 import QtGui
 
@@ -1590,7 +1590,7 @@ class PartGroup(Group):
         regularkids = Group.MT_kids(self, display_prefs)
         if 1 and self.open:
             #bruce 080306 test code, should clean up
-            from debug_prefs import debug_pref, Choice_boolean_False
+            from utilities.debug_prefs import debug_pref, Choice_boolean_False
             want_fake_kid = debug_pref("Model Tree: show fake initial kid?", Choice_boolean_False)
             have_fake_kid = not not self._initialkids
             if have_fake_kid and not want_fake_kid:
diff --git a/cad/src/model/bond_constants.py b/cad/src/model/bond_constants.py
index 8cd424212..45f8f4464 100755
--- a/cad/src/model/bond_constants.py
+++ b/cad/src/model/bond_constants.py
@@ -23,10 +23,10 @@ as for bond2.]
 from math import floor, ceil
 
 from geometry.VQT import Q
-from debug import print_compact_traceback    
+from utilities.debug import print_compact_traceback    
 from utilities import debug_flags
 import foundation.env as env
-from PyrexSimulator import thePyrexSimulator
+from simulation.PyrexSimulator import thePyrexSimulator
 
 # ==
 
diff --git a/cad/src/model/bonds.py b/cad/src/model/bonds.py
index 1c474c63b..7181d2f27 100755
--- a/cad/src/model/bonds.py
+++ b/cad/src/model/bonds.py
@@ -35,8 +35,8 @@ from Numeric import floor
 
 from geometry.VQT import Q, vlen, norm
 
-from debug import print_compact_stack, compact_stack, print_compact_traceback
-from debug import reload_once_per_event
+from utilities.debug import print_compact_stack, compact_stack, print_compact_traceback
+from utilities.debug import reload_once_per_event
 
 from utilities import debug_flags
 
@@ -52,18 +52,18 @@ from model.bond_constants import bond_type_names
 from model.bond_constants import atoms_are_bonded
 from model.bond_constants import find_bond
 
-from bond_chains import grow_directional_bond_chain
+from operations.bond_chains import grow_directional_bond_chain
 
 import model.global_model_changedicts as global_model_changedicts
 import foundation.env as env
 
-from GlobalPreferences import usePyrexAtomsAndBonds
+from utilities.GlobalPreferences import usePyrexAtomsAndBonds
 
 from foundation.state_utils import StateMixin, IdentityCopyMixin
 from foundation.state_utils import register_instancelike_class
 
 from foundation.changedicts import register_changedict, register_class_changedicts
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 from utilities.Log import redmsg, quote_html
 
 from foundation.state_constants import S_CACHE, S_DATA, S_PARENT, UNDO_SPECIALCASE_BOND
@@ -1914,9 +1914,9 @@ class Bond(BondBase, StateMixin, Selobj_API, IdentityCopyMixin):
         to order the atoms in the bond left-to-right (e.g. in text strings).
         """
         if debug_flags.atom_debug:
-            import bond_utils
+            import operations.bond_utils as bond_utils
             reload(bond_utils) # at least during development
-        from bond_utils import bond_menu_section
+        from operations.bond_utils import bond_menu_section
         return bond_menu_section(self, quat = quat)
 
     # ==
diff --git a/cad/src/model/chem.py b/cad/src/model/chem.py
index 894b745b3..02ef848e6 100755
--- a/cad/src/model/chem.py
+++ b/cad/src/model/chem.py
@@ -81,38 +81,38 @@ from geometry.VQT import atom_angle_radians
 from graphics.rendering.mdl.mdldata import marks, links, filler
 from graphics.rendering.povray.povheader import povpoint
 
-import debug
-from debug import print_compact_stack, print_compact_traceback
+import utilities.debug as debug
+from utilities.debug import print_compact_stack, print_compact_traceback
 ##from debug import compact_stack
-from debug_prefs import debug_pref, Choice_boolean_False, Choice
+from utilities.debug_prefs import debug_pref, Choice_boolean_False, Choice
 
 from foundation.changedicts import register_changedict, register_class_changedicts
 
 from utilities.Printing import Vector3ToString
 from utilities.Log import orangemsg, redmsg
 
-from constants import genKey
+from utilities.constants import genKey
 
-from constants import diDEFAULT
-from constants import diBALL
-from constants import diTrueCPK
-from constants import diTUBES
-from constants import diINVISIBLE
+from utilities.constants import diDEFAULT
+from utilities.constants import diBALL
+from utilities.constants import diTrueCPK
+from utilities.constants import diTUBES
+from utilities.constants import diINVISIBLE
 
-from constants import ATOM_CONTENT_FOR_DISPLAY_STYLE
+from utilities.constants import ATOM_CONTENT_FOR_DISPLAY_STYLE
 
-from constants import dispLabel
-from constants import default_display_mode
-from constants import TubeRadius
+from utilities.constants import dispLabel
+from utilities.constants import default_display_mode
+from utilities.constants import TubeRadius
 
-from constants import pink
-from constants import orange
+from utilities.constants import pink
+from utilities.constants import orange
 
-from constants import ErrorPickedColor
-from constants import PickedColor
+from utilities.constants import ErrorPickedColor
+from utilities.constants import PickedColor
 
-from GlobalPreferences import disable_do_not_draw_open_bonds
-from GlobalPreferences import usePyrexAtomsAndBonds
+from utilities.GlobalPreferences import disable_do_not_draw_open_bonds
+from utilities.GlobalPreferences import usePyrexAtomsAndBonds
 
 from model.bond_constants import V_SINGLE
 from model.bond_constants import min_max_valences_from_v6
@@ -123,11 +123,11 @@ from model.bond_constants import DIRBOND_CHAIN_END
 from model.bond_constants import DIRBOND_NONE
 from model.bond_constants import DIRBOND_ERROR
 
-from prefs_constants import arrowsOnFivePrimeEnds_prefs_key
-from prefs_constants import arrowsOnThreePrimeEnds_prefs_key
-from prefs_constants import showValenceErrors_prefs_key
-from prefs_constants import cpkScaleFactor_prefs_key
-from prefs_constants import diBALL_AtomRadius_prefs_key
+from utilities.prefs_constants import arrowsOnFivePrimeEnds_prefs_key
+from utilities.prefs_constants import arrowsOnThreePrimeEnds_prefs_key
+from utilities.prefs_constants import showValenceErrors_prefs_key
+from utilities.prefs_constants import cpkScaleFactor_prefs_key
+from utilities.prefs_constants import diBALL_AtomRadius_prefs_key
 
 from foundation.state_constants import S_CHILDREN, S_PARENT, S_DATA, S_CACHE
 from foundation.state_constants import UNDO_SPECIALCASE_ATOM, ATOM_CHUNK_ATTRIBUTE_NAME
@@ -137,7 +137,7 @@ from graphics.drawables.Selobj import Selobj_API
 
 from utilities import debug_flags
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
 import foundation.env as env
 
@@ -1374,7 +1374,7 @@ class Atom(AtomBase, InvalMixin, StateMixin, Selobj_API, IdentityCopyMixin):
         """
         assert self._f_draw_bond_geometry_error_indicator_externally # for now
         assert self.bond_geometry_error_string # make private??
-        from constants import ave_colors, red
+        from utilities.constants import ave_colors, red
         color = ave_colors(0.5, orange, red) # revise? 
         self.overdraw_with_special_color( color,
             factor = self._BOND_GEOM_ERROR_RADIUS_MULTIPLIER)
@@ -3616,7 +3616,7 @@ class Atom(AtomBase, InvalMixin, StateMixin, Selobj_API, IdentityCopyMixin):
         @warning: we assume baggage is a subset of self.baggageNeighbors(), but don't check this except when ATOM_DEBUG is set.
         """
         try:
-            import reposition_baggage
+            import operations.reposition_baggage as reposition_baggage
             debug.reload_once_per_event(reposition_baggage) # this can be removed when devel is done, but doesn't need to be
             reposition_baggage.reposition_baggage_0(self, baggage, planned_atom_nupos)
         except:
diff --git a/cad/src/model/chunk.py b/cad/src/model/chunk.py
index 9f7a3d37d..5e97fcd62 100755
--- a/cad/src/model/chunk.py
+++ b/cad/src/model/chunk.py
@@ -75,14 +75,14 @@ from foundation.NodeWithAtomContents import NodeWithAtomContents
 
 from utilities.Log import orangemsg, redmsg, quote_html, graymsg
 
-from debug import print_compact_stack, print_compact_traceback, safe_repr
+from utilities.debug import print_compact_stack, print_compact_traceback, safe_repr
 
 from foundation.inval import InvalMixin
 from foundation.changes import SelfUsageTrackingMixin, SubUsageTrackingMixin
     #bruce 050804, so glpanes can know when they need to redraw a chunk's display list,
     # and chunks can know when they need to inval that because something drawn into it
     # would draw differently due to a change in some graphics pref it used
-from prefs_constants import bondpointHotspotColor_prefs_key
+from utilities.prefs_constants import bondpointHotspotColor_prefs_key
 import foundation.env as env
 import graphics.drawing.drawer as drawer
 from foundation.undo_archive import set_undo_nullMol
@@ -94,9 +94,9 @@ from foundation.state_constants import S_REF, S_CHILDREN_NOT_DATA
 
 from utilities import debug_flags
 
-from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
 
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 import model.bonds as bonds # TODO: import specific functions, since no longer an import cycle
 
@@ -107,20 +107,20 @@ from graphics.drawing.drawer import ColorSorter, ColorSortedDisplayList
 ##from drawer import drawlinelist
 
 ##from constants import PickedColor
-from constants import darkgreen, yellow
+from utilities.constants import darkgreen, yellow
 
-from constants import gensym, genKey
+from utilities.constants import gensym, genKey
 
-from constants import diDEFAULT
-from constants import diINVISIBLE
-from constants import diBALL
-from constants import diLINES
-from constants import diTUBES
-from constants import diTrueCPK
-from constants import diDNACYLINDER
+from utilities.constants import diDEFAULT
+from utilities.constants import diINVISIBLE
+from utilities.constants import diBALL
+from utilities.constants import diLINES
+from utilities.constants import diTUBES
+from utilities.constants import diTrueCPK
+from utilities.constants import diDNACYLINDER
 
-from constants import ATOM_CONTENT_FOR_DISPLAY_STYLE
-from constants import noop
+from utilities.constants import ATOM_CONTENT_FOR_DISPLAY_STYLE
+from utilities.constants import noop
 
 from model.elements import PeriodicTable
 
@@ -128,7 +128,7 @@ from commands.ChunkProperties.ChunkProp import ChunkProp
 
 from dna.model.Dna_Constants import getComplementSequence
 
-from bond_chains import grow_directional_bond_chain
+from operations.bond_chains import grow_directional_bond_chain
 
 from graphics.drawing.drawer import apply_material, allow_color_sorting, use_color_sorted_dls
 
@@ -3778,7 +3778,7 @@ def debug_make_BorrowerChunk_raw(do_addmol = True):
     win.win_update() #k is this done by caller?
     return
 
-from debug import register_debug_menu_command
+from utilities.debug import register_debug_menu_command
 register_debug_menu_command("make BorrowerChunk", debug_make_BorrowerChunk)
 register_debug_menu_command("make BorrowerChunk (no addmol)", debug_make_BorrowerChunk_no_addmol)
 
diff --git a/cad/src/model/elements_data.py b/cad/src/model/elements_data.py
index 1cc541f80..faeb8f71d 100755
--- a/cad/src/model/elements_data.py
+++ b/cad/src/model/elements_data.py
@@ -22,7 +22,7 @@ Bruce 071105 revised init code, and split PAM3 and PAM5 data into separate files
 """
 
 from geometry.VQT import V, A, norm
-from constants import DIAMOND_BOND_LENGTH
+from utilities.constants import DIAMOND_BOND_LENGTH
 
 _DIRECTIONAL_BOND_ELEMENTS_chemical = ('X',) # mark 071014
 
diff --git a/cad/src/model/jigs.py b/cad/src/model/jigs.py
index 13f7265ba..d86321a08 100755
--- a/cad/src/model/jigs.py
+++ b/cad/src/model/jigs.py
@@ -43,22 +43,22 @@ from OpenGL.GL import GL_FILL
 from utilities import debug_flags
 
 from foundation.Utility import NodeWith3DContents
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 from geometry.VQT import A
 from commands.ThermostatProperties.StatProp import StatProp
 from commands.ThermometerProperties.ThermoProp import ThermoProp
 
 from utilities.Log import orangemsg
 from graphics.rendering.povray.povheader import povpoint
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 import foundation.env as env
 from graphics.drawing.drawer import drawwirecube
 
-from constants import gensym
-from constants import darkgreen
-from constants import blue
-from constants import darkred
-from constants import black
+from utilities.constants import gensym
+from utilities.constants import darkgreen
+from utilities.constants import blue
+from utilities.constants import darkred
+from utilities.constants import black
 from foundation.state_constants import S_REFS
 
 from graphics.drawables.Selobj import Selobj_API
@@ -415,7 +415,7 @@ class Jig(NodeWith3DContents, Selobj_API):
 
         [extends superclass method]
         """
-        from debug_prefs import debug_pref_History_print_every_selected_object
+        from utilities.debug_prefs import debug_pref_History_print_every_selected_object
         if debug_pref_History_print_every_selected_object(): #bruce 070504 added this condition
             env.history.message(self.getinfo())
                 #bruce 050901 revised this; now done even if jig is killed (might affect fixed bug 451-9)
diff --git a/cad/src/model/jigs_measurements.py b/cad/src/model/jigs_measurements.py
index de90692d6..1d0073381 100755
--- a/cad/src/model/jigs_measurements.py
+++ b/cad/src/model/jigs_measurements.py
@@ -31,14 +31,14 @@ import foundation.env as env
 from geometry.VQT import V, norm, cross, vlen, angleBetween
 from foundation.Utility import Node
 from utilities.Log import redmsg, greenmsg, orangemsg
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 from model.jigs import Jig
 from graphics.drawing.dimensions import drawLinearDimension, drawAngleDimension, drawDihedralDimension
 from graphics.drawing.drawer import drawtext
 
-from constants import black
-from prefs_constants import dynamicToolTipAtomDistancePrecision_prefs_key
-from prefs_constants import dynamicToolTipBendAnglePrecision_prefs_key
+from utilities.constants import black
+from utilities.prefs_constants import dynamicToolTipAtomDistancePrecision_prefs_key
+from utilities.prefs_constants import dynamicToolTipBendAnglePrecision_prefs_key
 
 def _constrainHandleToAngle(pos, p0, p1, p2):
     """
diff --git a/cad/src/model/jigs_motors.py b/cad/src/model/jigs_motors.py
index eb767108e..78dc6946b 100755
--- a/cad/src/model/jigs_motors.py
+++ b/cad/src/model/jigs_motors.py
@@ -34,10 +34,10 @@ from graphics.drawing.drawer import drawLinearSign
 from utilities.Log import orangemsg
 from utilities.Log import redmsg, greenmsg
 from graphics.rendering.povray.povheader import povpoint #bruce 050413
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 from model.jigs import Jig
 
-from constants import gray
+from utilities.constants import gray
 
 # == Motors
 
@@ -352,7 +352,7 @@ class RotaryMotor(Motor):
 
     def _getToolTipInfo(self): #ninad060825
         "Return a string for display in Dynamic Tool tip "
-        from PlatformDependent import fix_plurals
+        from platform.PlatformDependent import fix_plurals
         attachedAtomCount = fix_plurals("Attached to %d atom(s)"%(len(self.atoms)))
         return str(self.name) + "<br>" +  "<font color=\"#0000FF\"> Jig Type:</font>Rotary Motor"\
                +  "<br>" + "<font color=\"#0000FF\">Torque: </font>" + str(self.torque) +  " nN-nm " \
@@ -700,7 +700,7 @@ class LinearMotor(Motor):
 
     def _getToolTipInfo(self): #ninad060825
         "Return a string for display in Dynamic Tool tip "
-        from PlatformDependent import fix_plurals
+        from platform.PlatformDependent import fix_plurals
         attachedAtomCount = fix_plurals("Attached to %d atom(s)"%(len(self.atoms)))
         return str(self.name) + "<br>" +  "<font color=\"#0000FF\"> Jig Type:</font>Linear Motor"\
                +  "<br>" + "<font color=\"#0000FF\">Force: </font>" + str(self.force) +  " pN " \
diff --git a/cad/src/model/jigs_planes.py b/cad/src/model/jigs_planes.py
index db7f34f31..7d33a4e8a 100755
--- a/cad/src/model/jigs_planes.py
+++ b/cad/src/model/jigs_planes.py
@@ -36,11 +36,11 @@ from graphics.rendering.povray.povheader import povpoint
 
 from model.jigs import Jig
 
-from constants import black
-from constants import gray
+from utilities.constants import black
+from utilities.constants import gray
 
-from prefs_constants import SQUARE_GRID
-from prefs_constants import SOLID_LINE
+from utilities.prefs_constants import SQUARE_GRID
+from utilities.prefs_constants import SOLID_LINE
 
 from geometry.BoundingBox import BBox
 
diff --git a/cad/src/model/part.py b/cad/src/model/part.py
index 5ec0535d9..dae1201c5 100755
--- a/cad/src/model/part.py
+++ b/cad/src/model/part.py
@@ -54,7 +54,7 @@ from foundation.Assembly_API import Assembly_API
 
 from model.NamedView import NamedView
 from geometry.VQT import V, Q
-from debug import print_compact_traceback, print_compact_stack
+from utilities.debug import print_compact_traceback, print_compact_stack
 from utilities import debug_flags
 
 from utilities.Log import greenmsg, redmsg
@@ -64,24 +64,24 @@ from model.chunk import Chunk
 from model.jigs import Jig
 from foundation.node_indices import fix_one_or_complain
 
-from constants import diINVISIBLE
+from utilities.constants import diINVISIBLE
 
 import foundation.env as env
 
 from foundation.inval import InvalMixin
 from foundation.state_utils import StateMixin, IdentityCopyMixin
-from jigmakers_Mixin import jigmakers_Mixin
-from ops_atoms     import ops_atoms_Mixin
-from ops_connected import ops_connected_Mixin
-from ops_copy      import ops_copy_Mixin
-from ops_motion    import ops_motion_Mixin
-from ops_rechunk   import ops_rechunk_Mixin
-from ops_select    import ops_select_Mixin
-
-from constants import diDEFAULT
-from constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
+from operations.jigmakers_Mixin import jigmakers_Mixin
+from operations.ops_atoms import ops_atoms_Mixin
+from operations.ops_connected import ops_connected_Mixin
+from operations.ops_copy import ops_copy_Mixin
+from operations.ops_motion import ops_motion_Mixin
+from operations.ops_rechunk import ops_rechunk_Mixin
+from operations.ops_select import ops_select_Mixin
+
+from utilities.constants import diDEFAULT
+from utilities.constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
 from foundation.state_constants import S_REF, S_DATA, S_PARENT, S_CHILD
-from prefs_constants import levelOfDetail_prefs_key
+from utilities.prefs_constants import levelOfDetail_prefs_key
 
 from model.Line import Line
 
diff --git a/cad/src/model/pi_bond_sp_chain.py b/cad/src/model/pi_bond_sp_chain.py
index 773671633..174f1d729 100755
--- a/cad/src/model/pi_bond_sp_chain.py
+++ b/cad/src/model/pi_bond_sp_chain.py
@@ -30,7 +30,7 @@ from utilities import debug_flags
 from model.jigs import Jig
 from geometry.VQT import V, Q, A, cross, vlen, norm, twistor_angle
 
-from bond_chains import grow_bond_chain
+from operations.bond_chains import grow_bond_chain
 
 from model.bond_constants import V_SINGLE
 from model.bond_constants import V_DOUBLE
diff --git a/cad/src/model/prefsTree.py b/cad/src/model/prefsTree.py
index 307b46be5..41d6f09b9 100755
--- a/cad/src/model/prefsTree.py
+++ b/cad/src/model/prefsTree.py
@@ -23,7 +23,7 @@ import os
 from foundation.Utility import Node
 from foundation.Group import Group
 from model.part import Part
-from constants import noop, dispLabel, default_display_mode
+from utilities.constants import noop, dispLabel, default_display_mode
 import foundation.env as env
 
 _debug_prefstree = True # safe for commit even when True
@@ -199,7 +199,7 @@ def read_mmp_single_part(assy, filename):
         # It depends on there being only one active history object at a time.
         # (Before 050913, that object was stored as both env.history and win.history.)
     oldmessage = history.message
-    from constants import noop
+    from utilities.constants import noop
     history.message = noop # don't bother user with this file being nonstd (bad, should pass a flag, so other errors seen)
     try:
         grouplist  = readmmp(assy, filename, isInsert = True)
diff --git a/cad/src/modelTree/ModelTree.py b/cad/src/modelTree/ModelTree.py
index 71064c299..e3c6d9ca7 100755
--- a/cad/src/modelTree/ModelTree.py
+++ b/cad/src/modelTree/ModelTree.py
@@ -41,24 +41,24 @@ from PyQt4 import QtCore
 
 import foundation.env as env
 from utilities import debug_flags
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 import modelTree.modelTreeGui as modelTreeGui # defines ModelTreeGui (note case difference), Ne1Model_api
 
 from model.chunk import Chunk
 from model.jigs import Jig
 from utilities.Log import orangemsg
 from foundation.Group import Group
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from GlobalPreferences import permit_atom_chunk_coselection
+from utilities.GlobalPreferences import permit_atom_chunk_coselection
 
-from constants import gensym
-from constants import SELWHAT_ATOMS
-from constants import SELWHAT_CHUNKS
-from constants import SELWHAT_NAMES
-from constants import noop
+from utilities.constants import gensym
+from utilities.constants import SELWHAT_ATOMS
+from utilities.constants import SELWHAT_CHUNKS
+from utilities.constants import SELWHAT_NAMES
+from utilities.constants import noop
 
-from qt4transition import qt4here
+from utilities.qt4transition import qt4here
 
 _debug_preftree = False # bruce 050602 experiment; do not commit with True
 
@@ -685,7 +685,7 @@ class modelTree(modelTreeGui.Ne1Model_api):
 
         # figure out whether Copy would actually copy anything.
         part = nodeset[0].part # the same for all nodes in nodeset
-        from ops_select import selection_from_part
+        from operations.ops_select import selection_from_part
         sel = selection_from_part(part, use_selatoms = False) #k should this be the first code to use selection_from_MT() instead?
         doit = False
         for node in nodeset:
@@ -803,7 +803,7 @@ class modelTree(modelTreeGui.Ne1Model_api):
         self.assy.Unhide() # includes win_update
 
     def cm_set_node(self): #bruce 050604, for debugging
-        import debug
+        import utilities.debug as debug
         nodeset = self.modelTreeGui.topmost_selected_nodes()
         if len(nodeset) == 1:
             debug._node = nodeset[0]
diff --git a/cad/src/modelTree/Node_as_MT_DND_Target.py b/cad/src/modelTree/Node_as_MT_DND_Target.py
index af6e57548..13525800c 100644
--- a/cad/src/modelTree/Node_as_MT_DND_Target.py
+++ b/cad/src/modelTree/Node_as_MT_DND_Target.py
@@ -30,8 +30,8 @@ described in the bug report.
 from foundation.Group import Group # for isinstance and for autogrouping; could remove by
     # asking the assy (and/or the dropped on node) to do the grouping
 
-from ops_copy import copy_nodes_in_order
-from ops_copy import copied_nodes_for_DND
+from operations.ops_copy import copy_nodes_in_order
+from operations.ops_copy import copied_nodes_for_DND
 
 import foundation.env as env
 
diff --git a/cad/src/modelTree/modelTreeGui.py b/cad/src/modelTree/modelTreeGui.py
index a899e907e..c36ae3420 100755
--- a/cad/src/modelTree/modelTreeGui.py
+++ b/cad/src/modelTree/modelTreeGui.py
@@ -67,19 +67,19 @@ from PyQt4.Qt import SIGNAL
 from PyQt4.Qt import QApplication
 from PyQt4.Qt import QPalette
 
-from debug import print_compact_traceback, print_compact_stack
-from PlatformDependent import fix_plurals
+from utilities.debug import print_compact_traceback, print_compact_stack
+from platform.PlatformDependent import fix_plurals
 from utilities.Log import quote_html
-from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False, Choice
-from menu_helpers import makemenu_helper
+from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False, Choice
+from widgets.menu_helpers import makemenu_helper
 import foundation.env as env
 
 from widgets.simple_dialogs import grab_text_line_using_dialog
-from icon_utilities import imagename_to_pixmap
+from utilities.icon_utilities import imagename_to_pixmap
 
 from modelTree.Node_as_MT_DND_Target import Node_as_MT_DND_Target #bruce 071025
 
-from constants import AC_INVISIBLE, AC_HAS_INDIVIDUAL_DISPLAY_STYLE
+from utilities.constants import AC_INVISIBLE, AC_HAS_INDIVIDUAL_DISPLAY_STYLE
 
 DEBUG0 = False # debug api compliance
 DEBUG = False # debug selection stuff
@@ -251,7 +251,7 @@ class Ne1Model_api(Api):
         [But not including any children of selected nodes. --bruce]
         """
         nodes = [self.get_current_part_topnode()]
-        from ops_select import topmost_selected_nodes
+        from operations.ops_select import topmost_selected_nodes
         return topmost_selected_nodes(nodes)
 
     pass # end of class Ne1Model_api
@@ -1599,7 +1599,7 @@ class MT_View(QtGui.QWidget):
         self.modeltreegui.mt_update()
     
     def get_icons(self):
-        from icon_utilities import getpixmap
+        from utilities.icon_utilities import getpixmap
         # note: geticon calls QIcon, but painter has no drawIcon, and drawPixmap doesn't accept them,
         # so here we use getpixmap which calls QPixmap. We could also try QImage and painter.drawImage
         # (known to work for crate.bmp and other test images, but presumably slower).
@@ -1893,7 +1893,7 @@ class ModelTreeGui(QScrollArea, ModelTreeGui_common):
         self.setWidget(self.view)
         
         # Model Tree background color. Mark 2007-06-04
-        from prefs_constants import mtColor_prefs_key # In case we want to make it a user pref.
+        from utilities.prefs_constants import mtColor_prefs_key # In case we want to make it a user pref.
         from widgets.widget_helpers import RGBf_to_QColor
         mtColor = RGBf_to_QColor(env.prefs[mtColor_prefs_key]) 
         from PM.PM_Colors  import getPalette
diff --git a/cad/src/model_updater/bond_updater.py b/cad/src/model_updater/bond_updater.py
index 5c7728f18..d6e431c5a 100755
--- a/cad/src/model_updater/bond_updater.py
+++ b/cad/src/model_updater/bond_updater.py
@@ -25,7 +25,7 @@ part of this into master_model_updater.py, leaving only the bond-
 type- and atom-type- updating code in this file.
 """
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from model.bond_constants import V_SINGLE
 from model.bond_constants import V_DOUBLE
diff --git a/cad/src/model_updater/master_model_updater.py b/cad/src/model_updater/master_model_updater.py
index 6da2037d9..8843b895f 100755
--- a/cad/src/model_updater/master_model_updater.py
+++ b/cad/src/model_updater/master_model_updater.py
@@ -51,7 +51,7 @@ from utilities.Log import redmsg
 from model_updater.bond_updater import update_bonds_after_each_event
 from model_updater.bond_updater import process_changed_bond_types
 
-from debug import print_compact_stack, print_compact_traceback
+from utilities.debug import print_compact_stack, print_compact_traceback
 
 # ==
 
@@ -213,7 +213,7 @@ def _autodelete_empty_groups(assy): #bruce 080305
 # temporary code for use while developing dna_updater
 
 def debug_pref_autodelete_empty_groups():
-    from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
     res = debug_pref("autodelete empty groups?",
                      ##Choice_boolean_False,
                      #autodelete empty groups by default. This looks safe so far
@@ -226,7 +226,7 @@ def debug_pref_autodelete_empty_groups():
     return res
 
 def debug_pref_use_dna_updater():
-    from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
     res = debug_pref("DNA: use dna_updater.py?",
                      Choice_boolean_False,
                      ## SOON: Choice_boolean_True,
@@ -235,10 +235,10 @@ def debug_pref_use_dna_updater():
     return res
 
 def debug_pref_reload_dna_updater():
-    import EndUser
+    import utilities.EndUser as EndUser
     if not EndUser.enableDeveloperFeatures():
         return False
-    from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False
     res = debug_pref("DNA: auto-reload dna_updater.py?",
                      Choice_boolean_False,
                      ## SOON: Choice_boolean_True,
diff --git a/cad/src/ne1_startup/main_startup.py b/cad/src/ne1_startup/main_startup.py
index d53c43e23..845305e75 100755
--- a/cad/src/ne1_startup/main_startup.py
+++ b/cad/src/ne1_startup/main_startup.py
@@ -80,7 +80,7 @@ def startup_script( main_globals):
 
     # do some imports used for putting up splashscreen
     
-    import icon_utilities
+    import utilities.icon_utilities as icon_utilities
     icon_utilities.initialize() 
 
 
@@ -187,7 +187,7 @@ def startup_script( main_globals):
         #bruce 070515 added condition to disable this on Mac, until Brian fixes the hang on Mac.
         # Note: this is enabled in the Mac released version, due to a patch during the release
         # building process, at least in A9.1.
-        from Sponsors import PermissionDialog
+        from sponsors.Sponsors import PermissionDialog
 ##        print "start sponsors startup code"
         # Show the dialog that asks permission to download the sponsor logos, then
         # launch it as a thread to download and process the logos.
diff --git a/cad/src/ne1_startup/startup_before_most_imports.py b/cad/src/ne1_startup/startup_before_most_imports.py
index 1be02ee52..29f382b51 100644
--- a/cad/src/ne1_startup/startup_before_most_imports.py
+++ b/cad/src/ne1_startup/startup_before_most_imports.py
@@ -17,7 +17,7 @@ this new file startup/startup_before_most_imports.py.
 
 import sys, os
 
-import EndUser
+import utilities.EndUser as EndUser
 
 # NOTE: this module (or EndUser) must not do toplevel imports of our other
 # source modules, because it contains functions which need to be called
@@ -34,7 +34,7 @@ def before_most_imports( main_globals ):
 
     # gpl_only check at startup [bruce 041217]
     try:
-        import gpl_only as _gpl_only
+        import platform.gpl_only as _gpl_only
             # if this module is there, this lets it verify it should be there,
             # and if not, complain (to developers) whenever the program starts
         print "(running a GPL distribution)" #e retain or zap this?
@@ -46,7 +46,7 @@ def before_most_imports( main_globals ):
         rc = os.path.expanduser(rc)
         if os.path.exists(rc):
             ## execfile(rc) -- not allowed!
-            import debug as _debug
+            import utilities.debug as _debug
             _debug.legally_execfile_in_globals(rc, main_globals, error_exception = False)
                 # might fail in non-GPL versions; prints error message but
                 # does not raise an exception.
diff --git a/cad/src/ne1_startup/startup_misc.py b/cad/src/ne1_startup/startup_misc.py
index 01369ef7d..e3799858c 100755
--- a/cad/src/ne1_startup/startup_misc.py
+++ b/cad/src/ne1_startup/startup_misc.py
@@ -17,7 +17,7 @@ this new file startup/startup_misc.py.
 
 # note: toplevel imports are now ok in this module [bruce 071008 change]
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 def call_module_init_functions(): #bruce 071005 split this out of main_startup.startup_script
     """
@@ -45,7 +45,7 @@ def call_module_init_functions(): #bruce 071005 split this out of main_startup.s
     import model.assembly
     model.assembly.assembly.initialize()
     
-    import GroupButtonMixin
+    import PM.GroupButtonMixin as GroupButtonMixin
     GroupButtonMixin.GroupButtonMixin.initialize()
 
     return
@@ -88,7 +88,7 @@ def pre_main_show( win):
     #  screen size even on a very small screen.]
     # [bruce 050118 further modified this and removed some older comments
     #  (see cvs for those); also split out some code into platform.py.]
-    from PlatformDependent import screen_pos_size
+    from platform.PlatformDependent import screen_pos_size
     ((x0, y0), (screen_w, screen_h)) = screen_pos_size()
     # note: y0 is nonzero on mac, due to menubar at top of screen.
     
@@ -122,11 +122,11 @@ def pre_main_show( win):
 
     # After the above (whose side effects on main window geom. are used as defaults by the following code),
     # load any mainwindow geometry present in prefs db. [bruce 051218 new feature; see also new "save" features in UserPrefs.py]
-    from debug import print_compact_stack
+    from utilities.debug import print_compact_stack
     try:
         # this code is similar to debug.py's _debug_load_window_layout
         from ne1_ui.UserPrefs import load_window_pos_size
-        from prefs_constants import mainwindow_geometry_prefs_key_prefix
+        from utilities.prefs_constants import mainwindow_geometry_prefs_key_prefix
         keyprefix = mainwindow_geometry_prefs_key_prefix
         load_window_pos_size( win, keyprefix)
         win._ok_to_autosave_geometry_changes = True
@@ -161,7 +161,7 @@ def _initialize_custom_display_modes(win):
     
     # diCYLINDER
     import graphics.display_styles.CylinderChunks as CylinderChunks #bruce 060609
-    from debug_prefs import debug_pref, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_False
     enable_CylinderChunks = debug_pref("enable CylinderChunks next session?",
                                       Choice_boolean_False, 
                                       non_debug = True, 
@@ -231,7 +231,7 @@ def _init_experimental_commands():
 def _init_command_Atom_Generator(): 
     # TODO: this function should be moved into AtomGenerator.py
     # Atom Generator debug pref. Mark and Jeff. 2007-06-13
-    from debug_prefs import debug_pref, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_False
     from commands.BuildAtom.AtomGenerator import enableAtomGenerator
     _atomGeneratorIsEnabled = \
                     debug_pref("Atom Generator example code: enabled?", 
@@ -244,7 +244,7 @@ def _init_command_Atom_Generator():
 
 def _init_command_Peptide_Generator(): # piotr 080304 
     # This function enables an experimental peptide generator.
-    from debug_prefs import debug_pref, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_False
     from commands.InsertPeptide.PeptideGenerator import enablePeptideGenerator
     _peptideGeneratorIsEnabled = \
                     debug_pref("Peptide Generator: enabled?", 
@@ -259,17 +259,17 @@ def _init_command_Select_Bad_Atoms():
     # note: I think this was imported at one point
     # (which initialized it), and then got left out of the startup code
     # by mistake for awhile, when init code was revised. [bruce 071008]
-    import chem_patterns
+    import operations.chem_patterns as chem_patterns
     chem_patterns.initialize()
     return
 
 def _init_test_commands():
     #bruce 070613 
-    from debug_prefs import debug_pref, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_False
     if debug_pref("test_commands enabled (next session)", 
                   Choice_boolean_False, 
                   prefs_key = True):
-        import test_commands_init
+        import prototype.test_commands_init as test_commands_init
         test_commands_init.initialize()
     return
 
@@ -312,7 +312,7 @@ def _set_mainwindow_splitter_position( win):
     # Note: the resize is visible at startup.
     
     pw = win.activePartWindow()
-    from PropMgr_Constants import pmDefaultWidth
+    from PM.PropMgr_Constants import pmDefaultWidth
     w1, w2 = pw.pwSplitter.sizes()
     magic_combined_width = w1 + w2
     new_glpane_width = magic_combined_width - pmDefaultWidth
diff --git a/cad/src/ne1_ui/MWsemantics.py b/cad/src/ne1_ui/MWsemantics.py
index 9fb148f7b..a4381ad71 100755
--- a/cad/src/ne1_ui/MWsemantics.py
+++ b/cad/src/ne1_ui/MWsemantics.py
@@ -20,7 +20,7 @@ split up the class MWsemantics (as for cookieMode), not just the file.]
 """
 
 ##from qt4transition import qt4todo
-from qt4transition import qt4warning
+from utilities.qt4transition import qt4warning
 
 from PyQt4 import QtGui, QtCore
 
@@ -49,15 +49,15 @@ import time
 
 from utilities import debug_flags
 
-from PlatformDependent import find_or_make_Nanorex_directory
+from platform.PlatformDependent import find_or_make_Nanorex_directory
 ##from PlatformDependent import make_history_filename
-from PlatformDependent import open_file_in_editor
-from PlatformDependent import find_or_make_Nanorex_subdir
+from platform.PlatformDependent import open_file_in_editor
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
 
 from ne1_ui.ViewOrientationWindow import ViewOrientationWindow # Ninad 061121
 
-from debug import print_compact_traceback
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug import print_compact_traceback
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 from ne1_ui.Ui_MainWindow import Ui_MainWindow
 from ne1_ui.Ui_PartWindow import Ui_PartWindow
@@ -69,28 +69,28 @@ from utilities.Log import greenmsg, redmsg, orangemsg
 import ne1_ui.toolbars.Ui_CntFlyout as Ui_CntFlyout
 import ne1_ui.toolbars.Ui_DnaFlyout as Ui_DnaFlyout
 
-from ops_files import fileSlotsMixin
-from ops_view import viewSlotsMixin
-from ops_display import displaySlotsMixin
-from ops_modify import modifySlotsMixin 
+from operations.ops_files import fileSlotsMixin
+from operations.ops_view import viewSlotsMixin
+from operations.ops_display import displaySlotsMixin
+from operations.ops_modify import modifySlotsMixin 
 
 from foundation.changes import register_postinit_object
 import foundation.preferences as preferences
 import foundation.env as env 
 import foundation.undo_internals as undo_internals
 
-from prefs_constants import nanohive_enabled_prefs_key
-from prefs_constants import gamess_enabled_prefs_key
-from prefs_constants import gromacs_enabled_prefs_key
-from prefs_constants import cpp_enabled_prefs_key
-from prefs_constants import zoomAboutScreenCenter_prefs_key
-from prefs_constants import workingDirectory_prefs_key
-from prefs_constants import getDefaultWorkingDirectory
-from prefs_constants import rememberWinPosSize_prefs_key
-from prefs_constants import captionPrefix_prefs_key
-from prefs_constants import captionSuffix_prefs_key
-from prefs_constants import captionFullPath_prefs_key
-from prefs_constants import displayRulers_prefs_key
+from utilities.prefs_constants import nanohive_enabled_prefs_key
+from utilities.prefs_constants import gamess_enabled_prefs_key
+from utilities.prefs_constants import gromacs_enabled_prefs_key
+from utilities.prefs_constants import cpp_enabled_prefs_key
+from utilities.prefs_constants import zoomAboutScreenCenter_prefs_key
+from utilities.prefs_constants import workingDirectory_prefs_key
+from utilities.prefs_constants import getDefaultWorkingDirectory
+from utilities.prefs_constants import rememberWinPosSize_prefs_key
+from utilities.prefs_constants import captionPrefix_prefs_key
+from utilities.prefs_constants import captionSuffix_prefs_key
+from utilities.prefs_constants import captionFullPath_prefs_key
+from utilities.prefs_constants import displayRulers_prefs_key
 
 eCCBtab1 = [1,2, 5,6,7,8,9,10, 13,14,15,16,17,18, 32,33,34,35,36, 51,52,53,54]
 
@@ -681,7 +681,7 @@ class MWsemantics(QMainWindow,
         try:
             # wware 060406 bug 1263 - signal the simulator that we are exiting
             # (bruce 070618 moved this here from 3 places in prepareToCloseAndExit.)
-            from runSim import SimRunner
+            from simulation.runSim import SimRunner
             SimRunner.PREPARE_TO_CLOSE = True
         except:
             print_compact_traceback( msg )
@@ -830,7 +830,7 @@ class MWsemantics(QMainWindow,
         Slot for making a checkpoint (only available when Automatic 
         Checkpointing is disabled).
         """
-        import undo_UI
+        import operations.undo_UI as undo_UI
         undo_UI.editMakeCheckpoint(self)
         return
 
@@ -855,7 +855,7 @@ class MWsemantics(QMainWindow,
         """
         Slot for clearing the Undo Stack. Requires the user to confirm.
         """
-        import undo_UI
+        import operations.undo_UI as undo_UI
         undo_UI.editClearUndoStack(self)
         return
 
@@ -1011,7 +1011,7 @@ class MWsemantics(QMainWindow,
         """
         _cmd = greenmsg("Rename: ")
 
-        from ops_select import objectSelected, ATOMS, CHUNKS, JIGS
+        from operations.ops_select import objectSelected, ATOMS, CHUNKS, JIGS
         if not objectSelected(self.assy, objectFlags = CHUNKS | JIGS):
             if objectSelected(self.assy, objectFlags = ATOMS):
                 _msg = redmsg("Cannot rename atoms.")
@@ -1231,7 +1231,7 @@ class MWsemantics(QMainWindow,
         """
         Displays information about this version of NanoEngineer-1.
         """
-        from version import Version
+        from utilities.version import Version
         v = Version()
         product = v.product
         versionString = repr(v) + (" (%s)" % v.releaseType)
@@ -1321,9 +1321,9 @@ class MWsemantics(QMainWindow,
         """
         if debug_flags.atom_debug: #bruce 060106 added this (fixing trivial bug 1260)
             print "atom_debug: reloading runSim on each use, for development"
-            import runSim
+            import simulation.runSim as runSim
             reload(runSim)
-        from runSim import simSetup_CommandRun
+        from simulation.runSim import simSetup_CommandRun
         cmdrun = simSetup_CommandRun( self)
         cmdrun.run()
         return
@@ -1380,7 +1380,7 @@ class MWsemantics(QMainWindow,
 
         @note: This is not implemented.
         """
-        from ServerManager import ServerManager
+        from processes.ServerManager import ServerManager
         ServerManager().showDialog()
 
     ###################################
diff --git a/cad/src/ne1_ui/Ui_MainWindow.py b/cad/src/ne1_ui/Ui_MainWindow.py
index 2149e7f4f..f65123710 100755
--- a/cad/src/ne1_ui/Ui_MainWindow.py
+++ b/cad/src/ne1_ui/Ui_MainWindow.py
@@ -8,7 +8,7 @@ $Id$
 from PyQt4 import QtCore, QtGui
 from PyQt4.Qt import Qt, QWidget, QVBoxLayout
 
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 import ne1_ui.Ui_MainWindowWidgets as Ui_MainWindowWidgets
 import ne1_ui.Ui_MainWindowWidgetConnections as Ui_MainWindowWidgetConnections
@@ -32,7 +32,7 @@ import ne1_ui.toolbars.Ui_BuildToolsToolBar as Ui_BuildToolsToolBar
 import ne1_ui.toolbars.Ui_BuildStructuresToolBar as Ui_BuildStructuresToolBar
 import ne1_ui.toolbars.Ui_RenderingToolBar as Ui_RenderingToolBar
 
-from StatusBar import StatusBar
+from widgets.StatusBar import StatusBar
 
 import foundation.env as env
 
@@ -147,7 +147,7 @@ class Ui_MainWindow(object):
         # I intend to completely remove it soon. Mark 2008-02-29.
         Ui_BuildStructuresToolBar.setupUi(self, toolbarArea)
         
-        from prefs_constants import toolbar_state_prefs_key
+        from utilities.prefs_constants import toolbar_state_prefs_key
         # This fixes bug 2482.
         if not env.prefs[toolbar_state_prefs_key] == 'defaultToolbarState':
             # Restore the state of the toolbars from the last session.
diff --git a/cad/src/ne1_ui/Ui_MainWindowWidgets.py b/cad/src/ne1_ui/Ui_MainWindowWidgets.py
index 10c37e267..5b31b24da 100644
--- a/cad/src/ne1_ui/Ui_MainWindowWidgets.py
+++ b/cad/src/ne1_ui/Ui_MainWindowWidgets.py
@@ -18,8 +18,8 @@ History:
 import foundation.env as env
 from PyQt4 import QtGui
 from PyQt4.Qt import QToolButton
-from icon_utilities import geticon
-from prefs_constants import displayRulers_prefs_key
+from utilities.icon_utilities import geticon
+from utilities.prefs_constants import displayRulers_prefs_key
 
 def setupUi(win):
     """
diff --git a/cad/src/ne1_ui/Ui_PartWindow.py b/cad/src/ne1_ui/Ui_PartWindow.py
index 4478bb302..8a698bcdc 100755
--- a/cad/src/ne1_ui/Ui_PartWindow.py
+++ b/cad/src/ne1_ui/Ui_PartWindow.py
@@ -29,15 +29,15 @@ import os
 from PyQt4.Qt import Qt, QWidget, QFrame, QVBoxLayout, QSplitter
 from PyQt4.Qt import QTabWidget, QScrollArea, QSizePolicy
 from graphics.widgets.GLPane import GLPane
-from PropMgr_Constants import pmDefaultWidth, pmMaxWidth, pmMinWidth
-from icon_utilities import geticon
+from PM.PropMgr_Constants import pmDefaultWidth, pmMaxWidth, pmMinWidth
+from utilities.icon_utilities import geticon
 from modelTree.ModelTree import modelTree
-from qt4transition import qt4warnDestruction
+from utilities.qt4transition import qt4warnDestruction
 from utilities import debug_flags
 import foundation.env as env
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
-from prefs_constants import captionFullPath_prefs_key
+from utilities.prefs_constants import captionFullPath_prefs_key
 
 class _pwProjectTabWidget(QTabWidget):
     """
diff --git a/cad/src/ne1_ui/Ui_ReportsDockWidget.py b/cad/src/ne1_ui/Ui_ReportsDockWidget.py
index 750cd0658..c422b1d50 100644
--- a/cad/src/ne1_ui/Ui_ReportsDockWidget.py
+++ b/cad/src/ne1_ui/Ui_ReportsDockWidget.py
@@ -17,9 +17,9 @@ from PyQt4.Qt import Qt, QDockWidget, QWidget, QVBoxLayout, QTabWidget
 from PyQt4.Qt import QPalette, QSizePolicy
 from PM.PM_Colors import pmGrpBoxColor
 from PM.PM_Colors import getPalette
-from PlatformDependent import make_history_filename
-from qt4transition import qt4todo
-from prefs_constants import displayReportsWidget_prefs_key
+from platform.PlatformDependent import make_history_filename
+from utilities.qt4transition import qt4todo
+from utilities.prefs_constants import displayReportsWidget_prefs_key
 import foundation.env as env
 
 class Ui_ReportsDockWidget(QDockWidget):
diff --git a/cad/src/ne1_ui/Ui_ViewOrientation.py b/cad/src/ne1_ui/Ui_ViewOrientation.py
index 284003e03..498b0c547 100755
--- a/cad/src/ne1_ui/Ui_ViewOrientation.py
+++ b/cad/src/ne1_ui/Ui_ViewOrientation.py
@@ -5,7 +5,7 @@ $Id$
 
 from PyQt4 import QtCore, QtGui
 from PyQt4.Qt import Qt
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 
 class Ui_ViewOrientation:
diff --git a/cad/src/ne1_ui/UserPrefs.py b/cad/src/ne1_ui/UserPrefs.py
index 1eba80ee5..e503b27a8 100755
--- a/cad/src/ne1_ui/UserPrefs.py
+++ b/cad/src/ne1_ui/UserPrefs.py
@@ -35,141 +35,141 @@ from PyQt4.Qt import Qt
 
 from UserPrefsDialog import Ui_UserPrefsDialog
 import foundation.preferences as preferences
-from debug import print_compact_traceback
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug import print_compact_traceback
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 import foundation.env as env
 from widgets.widget_helpers import RGBf_to_QColor, QColor_to_RGBf
 from widgets.widget_helpers import double_fixup
-from prefs_widgets import connect_colorpref_to_colorframe, connect_checkbox_with_boolean_pref
+from widgets.prefs_widgets import connect_colorpref_to_colorframe, connect_checkbox_with_boolean_pref
 from utilities import debug_flags
-from PlatformDependent import screen_pos_size
-from PlatformDependent import get_rootdir
+from platform.PlatformDependent import screen_pos_size
+from platform.PlatformDependent import get_rootdir
 from graphics.rendering.povray.povray import get_default_plugin_path
-from icon_utilities import geticon
-
-from prefs_constants import displayCompass_prefs_key
-from prefs_constants import displayCompassLabels_prefs_key
-from prefs_constants import displayPOVAxis_prefs_key
-from prefs_constants import animateStandardViews_prefs_key
-from prefs_constants import displayVertRuler_prefs_key
-from prefs_constants import displayHorzRuler_prefs_key
-from prefs_constants import rulerPosition_prefs_key
-from prefs_constants import rulerColor_prefs_key
-from prefs_constants import rulerOpacity_prefs_key
-from prefs_constants import showRulersInPerspectiveView_prefs_key
-from prefs_constants import Adjust_watchRealtimeMinimization_prefs_key
-from prefs_constants import Adjust_minimizationEngine_prefs_key
-from prefs_constants import electrostaticsForDnaDuringAdjust_prefs_key
-from prefs_constants import Adjust_cutoverRMS_prefs_key
-from prefs_constants import qutemol_enabled_prefs_key
-from prefs_constants import qutemol_path_prefs_key
-from prefs_constants import nanohive_enabled_prefs_key
-from prefs_constants import nanohive_path_prefs_key
-from prefs_constants import povray_enabled_prefs_key
-from prefs_constants import povray_path_prefs_key
-from prefs_constants import megapov_enabled_prefs_key
-from prefs_constants import megapov_path_prefs_key
-from prefs_constants import povdir_enabled_prefs_key
-from prefs_constants import gamess_enabled_prefs_key
-from prefs_constants import gmspath_prefs_key
-from prefs_constants import gromacs_enabled_prefs_key
-from prefs_constants import gromacs_path_prefs_key
-from prefs_constants import cpp_enabled_prefs_key
-from prefs_constants import cpp_path_prefs_key
-from prefs_constants import defaultDisplayMode_prefs_key
-from prefs_constants import buildModeAutobondEnabled_prefs_key
-from prefs_constants import buildModeWaterEnabled_prefs_key
-from prefs_constants import buildModeHighlightingEnabled_prefs_key
-from prefs_constants import buildModeSelectAtomsOfDepositedObjEnabled_prefs_key
-from prefs_constants import light1Color_prefs_key
-from prefs_constants import light2Color_prefs_key
-from prefs_constants import light3Color_prefs_key
-from prefs_constants import atomHighlightColor_prefs_key
-from prefs_constants import bondpointHighlightColor_prefs_key
-from prefs_constants import levelOfDetail_prefs_key
-from prefs_constants import diBALL_AtomRadius_prefs_key
-from prefs_constants import cpkScaleFactor_prefs_key
-from prefs_constants import showBondStretchIndicators_prefs_key
-from prefs_constants import showValenceErrors_prefs_key
+from utilities.icon_utilities import geticon
+
+from utilities.prefs_constants import displayCompass_prefs_key
+from utilities.prefs_constants import displayCompassLabels_prefs_key
+from utilities.prefs_constants import displayPOVAxis_prefs_key
+from utilities.prefs_constants import animateStandardViews_prefs_key
+from utilities.prefs_constants import displayVertRuler_prefs_key
+from utilities.prefs_constants import displayHorzRuler_prefs_key
+from utilities.prefs_constants import rulerPosition_prefs_key
+from utilities.prefs_constants import rulerColor_prefs_key
+from utilities.prefs_constants import rulerOpacity_prefs_key
+from utilities.prefs_constants import showRulersInPerspectiveView_prefs_key
+from utilities.prefs_constants import Adjust_watchRealtimeMinimization_prefs_key
+from utilities.prefs_constants import Adjust_minimizationEngine_prefs_key
+from utilities.prefs_constants import electrostaticsForDnaDuringAdjust_prefs_key
+from utilities.prefs_constants import Adjust_cutoverRMS_prefs_key
+from utilities.prefs_constants import qutemol_enabled_prefs_key
+from utilities.prefs_constants import qutemol_path_prefs_key
+from utilities.prefs_constants import nanohive_enabled_prefs_key
+from utilities.prefs_constants import nanohive_path_prefs_key
+from utilities.prefs_constants import povray_enabled_prefs_key
+from utilities.prefs_constants import povray_path_prefs_key
+from utilities.prefs_constants import megapov_enabled_prefs_key
+from utilities.prefs_constants import megapov_path_prefs_key
+from utilities.prefs_constants import povdir_enabled_prefs_key
+from utilities.prefs_constants import gamess_enabled_prefs_key
+from utilities.prefs_constants import gmspath_prefs_key
+from utilities.prefs_constants import gromacs_enabled_prefs_key
+from utilities.prefs_constants import gromacs_path_prefs_key
+from utilities.prefs_constants import cpp_enabled_prefs_key
+from utilities.prefs_constants import cpp_path_prefs_key
+from utilities.prefs_constants import defaultDisplayMode_prefs_key
+from utilities.prefs_constants import buildModeAutobondEnabled_prefs_key
+from utilities.prefs_constants import buildModeWaterEnabled_prefs_key
+from utilities.prefs_constants import buildModeHighlightingEnabled_prefs_key
+from utilities.prefs_constants import buildModeSelectAtomsOfDepositedObjEnabled_prefs_key
+from utilities.prefs_constants import light1Color_prefs_key
+from utilities.prefs_constants import light2Color_prefs_key
+from utilities.prefs_constants import light3Color_prefs_key
+from utilities.prefs_constants import atomHighlightColor_prefs_key
+from utilities.prefs_constants import bondpointHighlightColor_prefs_key
+from utilities.prefs_constants import levelOfDetail_prefs_key
+from utilities.prefs_constants import diBALL_AtomRadius_prefs_key
+from utilities.prefs_constants import cpkScaleFactor_prefs_key
+from utilities.prefs_constants import showBondStretchIndicators_prefs_key
+from utilities.prefs_constants import showValenceErrors_prefs_key
 
 # DNA prefs
-from prefs_constants import bdnaBasesPerTurn_prefs_key
-from prefs_constants import bdnaRise_prefs_key
-from prefs_constants import dnaDefaultSegmentColor_prefs_key
-from prefs_constants import dnaColorBasesBy_prefs_key
-from prefs_constants import dnaStrutScaleFactor_prefs_key
-from prefs_constants import arrowsOnBackBones_prefs_key
-from prefs_constants import arrowsOnThreePrimeEnds_prefs_key
-from prefs_constants import arrowsOnFivePrimeEnds_prefs_key
+from utilities.prefs_constants import bdnaBasesPerTurn_prefs_key
+from utilities.prefs_constants import bdnaRise_prefs_key
+from utilities.prefs_constants import dnaDefaultSegmentColor_prefs_key
+from utilities.prefs_constants import dnaColorBasesBy_prefs_key
+from utilities.prefs_constants import dnaStrutScaleFactor_prefs_key
+from utilities.prefs_constants import arrowsOnBackBones_prefs_key
+from utilities.prefs_constants import arrowsOnThreePrimeEnds_prefs_key
+from utilities.prefs_constants import arrowsOnFivePrimeEnds_prefs_key
 
 # DNA style prefs 080310 piotr
-from prefs_constants import dnaStyleStrandsShape_prefs_key
-from prefs_constants import dnaStyleStrandsColor_prefs_key
-from prefs_constants import dnaStyleStrandsScale_prefs_key
-from prefs_constants import dnaStyleStrandsArrows_prefs_key
-from prefs_constants import dnaStyleAxisShape_prefs_key
-from prefs_constants import dnaStyleAxisColor_prefs_key
-from prefs_constants import dnaStyleAxisScale_prefs_key
-from prefs_constants import dnaStyleAxisTaper_prefs_key
-from prefs_constants import dnaStyleStrutsShape_prefs_key
-from prefs_constants import dnaStyleStrutsColor_prefs_key
-from prefs_constants import dnaStyleStrutsScale_prefs_key
-from prefs_constants import dnaStyleBasesShape_prefs_key
-from prefs_constants import dnaStyleBasesColor_prefs_key
-from prefs_constants import dnaStyleBasesScale_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsShape_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsColor_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsScale_prefs_key
+from utilities.prefs_constants import dnaStyleStrandsArrows_prefs_key
+from utilities.prefs_constants import dnaStyleAxisShape_prefs_key
+from utilities.prefs_constants import dnaStyleAxisColor_prefs_key
+from utilities.prefs_constants import dnaStyleAxisScale_prefs_key
+from utilities.prefs_constants import dnaStyleAxisTaper_prefs_key
+from utilities.prefs_constants import dnaStyleStrutsShape_prefs_key
+from utilities.prefs_constants import dnaStyleStrutsColor_prefs_key
+from utilities.prefs_constants import dnaStyleStrutsScale_prefs_key
+from utilities.prefs_constants import dnaStyleBasesShape_prefs_key
+from utilities.prefs_constants import dnaStyleBasesColor_prefs_key
+from utilities.prefs_constants import dnaStyleBasesScale_prefs_key
 
 # Undo prefs
-from prefs_constants import undoRestoreView_prefs_key
-from prefs_constants import undoAutomaticCheckpoints_prefs_key
-from prefs_constants import undoStackMemoryLimit_prefs_key
-from prefs_constants import historyMsgSerialNumber_prefs_key
-from prefs_constants import historyMsgTimestamp_prefs_key
-from prefs_constants import historyHeight_prefs_key
-from prefs_constants import rememberWinPosSize_prefs_key
-from prefs_constants import captionFullPath_prefs_key
-from prefs_constants import dynamicToolTipAtomChunkInfo_prefs_key
-from prefs_constants import dynamicToolTipAtomMass_prefs_key
-from prefs_constants import dynamicToolTipAtomPosition_prefs_key
-from prefs_constants import dynamicToolTipAtomDistanceDeltas_prefs_key
-from prefs_constants import dynamicToolTipBondLength_prefs_key
-from prefs_constants import dynamicToolTipBondChunkInfo_prefs_key
-from prefs_constants import dynamicToolTipAtomDistancePrecision_prefs_key
-from prefs_constants import captionPrefix_prefs_key
-from prefs_constants import captionSuffix_prefs_key
-from prefs_constants import compassPosition_prefs_key
-from prefs_constants import defaultProjection_prefs_key
-from prefs_constants import displayOriginAsSmallAxis_prefs_key
-from prefs_constants import displayOriginAxis_prefs_key
-from prefs_constants import animateMaximumTime_prefs_key
-from prefs_constants import mouseSpeedDuringRotation_prefs_key
-from prefs_constants import Adjust_endRMS_prefs_key
-from prefs_constants import Adjust_endMax_prefs_key
-from prefs_constants import Adjust_cutoverMax_prefs_key
-from prefs_constants import zoomAboutScreenCenter_prefs_key
-from prefs_constants import sponsor_permanent_permission_prefs_key
-from prefs_constants import sponsor_download_permission_prefs_key
-from prefs_constants import bondpointHotspotColor_prefs_key
-from prefs_constants import diBALL_bondcolor_prefs_key
-from prefs_constants import bondHighlightColor_prefs_key
-from prefs_constants import bondStretchColor_prefs_key
-from prefs_constants import bondVaneColor_prefs_key
-from prefs_constants import pibondStyle_prefs_key
-from prefs_constants import pibondLetters_prefs_key
-from prefs_constants import linesDisplayModeThickness_prefs_key
-from prefs_constants import diBALL_BondCylinderRadius_prefs_key
-from prefs_constants import startupMode_prefs_key
-from prefs_constants import defaultMode_prefs_key
-from prefs_constants import material_specular_highlights_prefs_key
-from prefs_constants import material_specular_shininess_prefs_key
-from prefs_constants import material_specular_brightness_prefs_key
-from prefs_constants import material_specular_finish_prefs_key
-from prefs_constants import povdir_path_prefs_key
-from prefs_constants import dynamicToolTipBendAnglePrecision_prefs_key
-from prefs_constants import dynamicToolTipVdwRadiiInAtomDistance_prefs_key
-from prefs_constants import displayFontPointSize_prefs_key
-from prefs_constants import useSelectedFont_prefs_key
-from prefs_constants import displayFont_prefs_key
-from prefs_constants import keepBondsDuringTransmute_prefs_key
+from utilities.prefs_constants import undoRestoreView_prefs_key
+from utilities.prefs_constants import undoAutomaticCheckpoints_prefs_key
+from utilities.prefs_constants import undoStackMemoryLimit_prefs_key
+from utilities.prefs_constants import historyMsgSerialNumber_prefs_key
+from utilities.prefs_constants import historyMsgTimestamp_prefs_key
+from utilities.prefs_constants import historyHeight_prefs_key
+from utilities.prefs_constants import rememberWinPosSize_prefs_key
+from utilities.prefs_constants import captionFullPath_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomChunkInfo_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomMass_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomPosition_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomDistanceDeltas_prefs_key
+from utilities.prefs_constants import dynamicToolTipBondLength_prefs_key
+from utilities.prefs_constants import dynamicToolTipBondChunkInfo_prefs_key
+from utilities.prefs_constants import dynamicToolTipAtomDistancePrecision_prefs_key
+from utilities.prefs_constants import captionPrefix_prefs_key
+from utilities.prefs_constants import captionSuffix_prefs_key
+from utilities.prefs_constants import compassPosition_prefs_key
+from utilities.prefs_constants import defaultProjection_prefs_key
+from utilities.prefs_constants import displayOriginAsSmallAxis_prefs_key
+from utilities.prefs_constants import displayOriginAxis_prefs_key
+from utilities.prefs_constants import animateMaximumTime_prefs_key
+from utilities.prefs_constants import mouseSpeedDuringRotation_prefs_key
+from utilities.prefs_constants import Adjust_endRMS_prefs_key
+from utilities.prefs_constants import Adjust_endMax_prefs_key
+from utilities.prefs_constants import Adjust_cutoverMax_prefs_key
+from utilities.prefs_constants import zoomAboutScreenCenter_prefs_key
+from utilities.prefs_constants import sponsor_permanent_permission_prefs_key
+from utilities.prefs_constants import sponsor_download_permission_prefs_key
+from utilities.prefs_constants import bondpointHotspotColor_prefs_key
+from utilities.prefs_constants import diBALL_bondcolor_prefs_key
+from utilities.prefs_constants import bondHighlightColor_prefs_key
+from utilities.prefs_constants import bondStretchColor_prefs_key
+from utilities.prefs_constants import bondVaneColor_prefs_key
+from utilities.prefs_constants import pibondStyle_prefs_key
+from utilities.prefs_constants import pibondLetters_prefs_key
+from utilities.prefs_constants import linesDisplayModeThickness_prefs_key
+from utilities.prefs_constants import diBALL_BondCylinderRadius_prefs_key
+from utilities.prefs_constants import startupMode_prefs_key
+from utilities.prefs_constants import defaultMode_prefs_key
+from utilities.prefs_constants import material_specular_highlights_prefs_key
+from utilities.prefs_constants import material_specular_shininess_prefs_key
+from utilities.prefs_constants import material_specular_brightness_prefs_key
+from utilities.prefs_constants import material_specular_finish_prefs_key
+from utilities.prefs_constants import povdir_path_prefs_key
+from utilities.prefs_constants import dynamicToolTipBendAnglePrecision_prefs_key
+from utilities.prefs_constants import dynamicToolTipVdwRadiiInAtomDistance_prefs_key
+from utilities.prefs_constants import displayFontPointSize_prefs_key
+from utilities.prefs_constants import useSelectedFont_prefs_key
+from utilities.prefs_constants import displayFont_prefs_key
+from utilities.prefs_constants import keepBondsDuringTransmute_prefs_key
 
 debug_sliders = False # Do not commit as True
 
@@ -231,7 +231,7 @@ def startup_commandName(): #bruce 060403
 
 def parentless_open_dialog_pref(): #bruce 060710 for Mac A8
     # see if setting this True fixes the Mac-specific bugs in draggability of this dialog, and CPU usage while it's up
-    from debug_prefs import debug_pref, Choice_boolean_False
+    from utilities.debug_prefs import debug_pref, Choice_boolean_False
     return debug_pref("parentless open file dialogs?", Choice_boolean_False,
                       prefs_key = "A8.1 devel/parentless open file dialogs")
 
@@ -1548,7 +1548,7 @@ restored when the user undoes a structural change.</p>
         self.current_height_spinbox.setValue(size[1])
 
         # Set string of Saved Size Lineedits
-        from prefs_constants import mainwindow_geometry_prefs_key_prefix
+        from utilities.prefs_constants import mainwindow_geometry_prefs_key_prefix
         keyprefix = mainwindow_geometry_prefs_key_prefix
         pos, size = _get_prefs_for_window_pos_size( self.w, keyprefix)
         self.update_saved_size(size[0], size[1])
@@ -1995,7 +1995,7 @@ restored when the user undoes a structural change.</p>
         self.w.showElementColorSettings(self)
 
     def usual_change_color(self, prefs_key, caption = "choose"): #bruce 050805
-        from prefs_widgets import colorpref_edit_dialog
+        from widgets.prefs_widgets import colorpref_edit_dialog
         colorpref_edit_dialog( self, prefs_key, caption = caption)
 
     def change_atom_hilite_color(self):
@@ -3120,7 +3120,7 @@ restored when the user undoes a structural change.</p>
         self.saved_height_lineedit.setText(QString(str(h) + " pixels"))
 
     def save_current_win_pos_and_size(self): #bruce 051218; see also debug.py's _debug_save_window_layout
-        from prefs_constants import mainwindow_geometry_prefs_key_prefix
+        from utilities.prefs_constants import mainwindow_geometry_prefs_key_prefix
         keyprefix = mainwindow_geometry_prefs_key_prefix
         save_window_pos_size( self.w, keyprefix) # prints history message
         size = self.w.size()
@@ -3131,7 +3131,7 @@ restored when the user undoes a structural change.</p>
         """
         Restore the window size, but not the position, from the prefs db.
         """
-        from prefs_constants import mainwindow_geometry_prefs_key_prefix
+        from utilities.prefs_constants import mainwindow_geometry_prefs_key_prefix
         keyprefix = mainwindow_geometry_prefs_key_prefix
         pos, size = _get_prefs_for_window_pos_size( self.w, keyprefix)
         w = size[0]
diff --git a/cad/src/ne1_ui/ViewOrientationWindow.py b/cad/src/ne1_ui/ViewOrientationWindow.py
index 1502b3040..58a3fb725 100755
--- a/cad/src/ne1_ui/ViewOrientationWindow.py
+++ b/cad/src/ne1_ui/ViewOrientationWindow.py
@@ -20,7 +20,7 @@ from PyQt4 import QtCore, QtGui
 from PyQt4.Qt import Qt, SIGNAL, QMainWindow, QDockWidget
 
 from ne1_ui.Ui_ViewOrientation import Ui_ViewOrientation
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 class ViewOrientationWindow(QDockWidget, Ui_ViewOrientation):
     
diff --git a/cad/src/ne1_ui/WhatsThisText_for_MainWindow.py b/cad/src/ne1_ui/WhatsThisText_for_MainWindow.py
index 5560e847f..a4ff15b94 100755
--- a/cad/src/ne1_ui/WhatsThisText_for_MainWindow.py
+++ b/cad/src/ne1_ui/WhatsThisText_for_MainWindow.py
@@ -140,7 +140,7 @@ def createWhatsThisTextForMainWindowWidgets(win):
 
     # Redo
 
-    from PlatformDependent import is_macintosh
+    from platform.PlatformDependent import is_macintosh
     if is_macintosh():
         redo_accel = "(Ctrl + Shift + Z)" # note: this is further 
                                           #modified (Ctrl -> Cmd) by other code
diff --git a/cad/src/ne1_ui/cursors.py b/cad/src/ne1_ui/cursors.py
index bdf4d4711..5d3b18250 100755
--- a/cad/src/ne1_ui/cursors.py
+++ b/cad/src/ne1_ui/cursors.py
@@ -17,7 +17,7 @@ self.o.setCursor(win.ArrowCursor)).
 from PyQt4.Qt import QCursor, QBitmap, Qt, QPainter
 import os, sys
 
-from icon_utilities import getCursorPixmap
+from utilities.icon_utilities import getCursorPixmap
 
 def loadCursors(w):
     """
diff --git a/cad/src/ne1_ui/help/help.py b/cad/src/ne1_ui/help/help.py
index cf96242ba..544782bdf 100755
--- a/cad/src/ne1_ui/help/help.py
+++ b/cad/src/ne1_ui/help/help.py
@@ -27,7 +27,7 @@ from PyQt4.Qt import QWidget
 from PyQt4.Qt import SIGNAL
 
 from ne1_ui.help.HelpDialog import Ui_HelpDialog
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 class Ne1HelpDialog(QWidget, Ui_HelpDialog):
     """
diff --git a/cad/src/ne1_ui/menus/Ui_BuildStructuresMenu.py b/cad/src/ne1_ui/menus/Ui_BuildStructuresMenu.py
index d08b6e0cb..cfb55fc7d 100755
--- a/cad/src/ne1_ui/menus/Ui_BuildStructuresMenu.py
+++ b/cad/src/ne1_ui/menus/Ui_BuildStructuresMenu.py
@@ -4,7 +4,7 @@ $Id$
 """
 
 from PyQt4 import QtGui
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 def setupUi(win):
     """
diff --git a/cad/src/ne1_ui/menus/Ui_InsertMenu.py b/cad/src/ne1_ui/menus/Ui_InsertMenu.py
index 3684814d4..61cde3033 100755
--- a/cad/src/ne1_ui/menus/Ui_InsertMenu.py
+++ b/cad/src/ne1_ui/menus/Ui_InsertMenu.py
@@ -4,7 +4,7 @@ $Id$
 """
 
 from PyQt4 import QtGui
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 def setupUi(win):
     """
diff --git a/cad/src/ne1_ui/menus/Ui_SimulationMenu.py b/cad/src/ne1_ui/menus/Ui_SimulationMenu.py
index f72b2c214..6d07b77f2 100755
--- a/cad/src/ne1_ui/menus/Ui_SimulationMenu.py
+++ b/cad/src/ne1_ui/menus/Ui_SimulationMenu.py
@@ -4,8 +4,8 @@ $Id$
 """
 
 from PyQt4 import QtGui
-from icon_utilities import geticon
-from debug_prefs  import debug_pref, Choice_boolean_False
+from utilities.icon_utilities import geticon
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 def setupUi(win):
     """
diff --git a/cad/src/ne1_ui/toolbars/Ui_BuildStructuresToolBar.py b/cad/src/ne1_ui/toolbars/Ui_BuildStructuresToolBar.py
index 4aa5f1aef..127535f87 100755
--- a/cad/src/ne1_ui/toolbars/Ui_BuildStructuresToolBar.py
+++ b/cad/src/ne1_ui/toolbars/Ui_BuildStructuresToolBar.py
@@ -5,7 +5,7 @@ $Id$
 
 from PyQt4 import QtGui
 from foundation.wiki_help import QToolBar_WikiHelp
-from debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
 
 def setupUi(win, toolbarArea):
     """
diff --git a/cad/src/ne1_ui/toolbars/Ui_CntFlyout.py b/cad/src/ne1_ui/toolbars/Ui_CntFlyout.py
index 37a47b1c8..7421bcc1f 100644
--- a/cad/src/ne1_ui/toolbars/Ui_CntFlyout.py
+++ b/cad/src/ne1_ui/toolbars/Ui_CntFlyout.py
@@ -19,7 +19,7 @@ import foundation.env as env
 from PyQt4 import QtCore, QtGui
 from PyQt4.Qt import Qt
 from PyQt4.Qt import SIGNAL
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from utilities.Log import greenmsg
 
 _theCntFlyout = None
diff --git a/cad/src/ne1_ui/toolbars/Ui_CommandToolbar.py b/cad/src/ne1_ui/toolbars/Ui_CommandToolbar.py
index a3c950ec1..bad1ed9b0 100755
--- a/cad/src/ne1_ui/toolbars/Ui_CommandToolbar.py
+++ b/cad/src/ne1_ui/toolbars/Ui_CommandToolbar.py
@@ -55,7 +55,7 @@ from PyQt4.Qt import QSpacerItem
 from PyQt4.Qt import QString
 from PyQt4.Qt import QPalette
 
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from foundation.wiki_help import QToolBar_WikiHelp
 from commandToolbar.CommandToolbar_Constants import cmdTbarCntrlAreaBtnColor
 from commandToolbar.CommandToolbar_Constants import cmdTbarSubCntrlAreaBtnColor
diff --git a/cad/src/ne1_ui/toolbars/Ui_DnaFlyout.py b/cad/src/ne1_ui/toolbars/Ui_DnaFlyout.py
index e99353380..1b344d9f7 100644
--- a/cad/src/ne1_ui/toolbars/Ui_DnaFlyout.py
+++ b/cad/src/ne1_ui/toolbars/Ui_DnaFlyout.py
@@ -16,7 +16,7 @@ import foundation.env as env
 from PyQt4 import QtCore, QtGui
 from PyQt4.Qt import Qt
 from PyQt4.Qt import SIGNAL
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from utilities.Log import greenmsg
 
 _theDnaFlyout = None
diff --git a/cad/src/operations/__init__.py b/cad/src/operations/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/operations/__init__.py
diff --git a/cad/src/bond_chains.py b/cad/src/operations/bond_chains.py
index 0f8465f9b..0f8465f9b 100644
--- a/cad/src/bond_chains.py
+++ b/cad/src/operations/bond_chains.py
diff --git a/cad/src/bond_utils.py b/cad/src/operations/bond_utils.py
index cc2e07d06..1770fb856 100755
--- a/cad/src/bond_utils.py
+++ b/cad/src/operations/bond_utils.py
@@ -14,10 +14,10 @@ created by bruce 050705 to help with higher-order bonds for Alpha6.
 """
 
 from geometry.VQT import Q
-from constants import noop
+from utilities.constants import noop
 import foundation.env as env
 from utilities.Log import greenmsg, redmsg, orangemsg, quote_html
-from debug import print_compact_stack
+from utilities.debug import print_compact_stack
 
 from model.bond_constants import bonded_atoms_summary
 from model.bond_constants import btype_from_v6
diff --git a/cad/src/bonds_from_atoms.py b/cad/src/operations/bonds_from_atoms.py
index a9114430d..e692915c8 100755
--- a/cad/src/bonds_from_atoms.py
+++ b/cad/src/operations/bonds_from_atoms.py
@@ -416,13 +416,13 @@ def inferBonds(mol): # [probably by Will; TODO: needs docstring]
                 removable[key2] = sing2
     for badGuy in removable.values():
         badGuy.kill()
-    from bonds_from_atoms import make_bonds
+    from operations.bonds_from_atoms import make_bonds
     make_bonds(mol.atoms.values())
     return
 
 # ==
 
-from debug import register_debug_menu_command
+from utilities.debug import register_debug_menu_command
 
 def remake_bonds_in_selection( glpane ):
     """
diff --git a/cad/src/chem_patterns.py b/cad/src/operations/chem_patterns.py
index 2bc618890..5c65b5c52 100755
--- a/cad/src/chem_patterns.py
+++ b/cad/src/operations/chem_patterns.py
@@ -16,9 +16,9 @@ Todo later:
 __author__ = "bruce"
 
 import foundation.env as env
-import debug
+import utilities.debug as debug
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 
 cmdname = "Select Bad Atoms"
 
diff --git a/cad/src/jigmakers_Mixin.py b/cad/src/operations/jigmakers_Mixin.py
index d1690a808..d1690a808 100644
--- a/cad/src/jigmakers_Mixin.py
+++ b/cad/src/operations/jigmakers_Mixin.py
diff --git a/cad/src/op_select_doubly.py b/cad/src/operations/op_select_doubly.py
index e915b712c..e915b712c 100755
--- a/cad/src/op_select_doubly.py
+++ b/cad/src/operations/op_select_doubly.py
diff --git a/cad/src/ops_atoms.py b/cad/src/operations/ops_atoms.py
index 752a19443..a9cb0b704 100755
--- a/cad/src/ops_atoms.py
+++ b/cad/src/operations/ops_atoms.py
@@ -14,9 +14,9 @@ from existing modules, from class Part and class basicMode.
 
 from utilities.Log import greenmsg, redmsg
 
-from constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
+from utilities.constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
 
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from model.elements import Singlet
 import foundation.env as env
 
diff --git a/cad/src/ops_connected.py b/cad/src/operations/ops_connected.py
index eeaf0be1b..77e6d7d9f 100755
--- a/cad/src/ops_connected.py
+++ b/cad/src/operations/ops_connected.py
@@ -59,7 +59,7 @@ class ops_connected_Mixin:
             else:
                 natoms += 1 # Counts atom that is already picked.
         
-        from PlatformDependent import fix_plurals
+        from platform.PlatformDependent import fix_plurals
         info = fix_plurals( "%d new atom(s) selected." % natoms)
         env.history.message( cmd + info)
         self.o.gl_update()
@@ -91,7 +91,7 @@ class ops_connected_Mixin:
                     # Just in case a selection filter was applied to this atom.
                     natoms += 1 
         
-        from PlatformDependent import fix_plurals
+        from platform.PlatformDependent import fix_plurals
         info = fix_plurals( "%d atom(s) unselected." % natoms)
         env.history.message( cmd + info)
         self.o.gl_update()
@@ -135,7 +135,7 @@ class ops_connected_Mixin:
             natoms += 1
             atom.kill()
         
-        from PlatformDependent import fix_plurals
+        from platform.PlatformDependent import fix_plurals
         info = fix_plurals( "%d connected atom(s) deleted." % natoms)
             #bruce 060331 comment: this message is sometimes wrong, since caller has deleted some atoms on click 1 of
             # a double click, and then calls us on click 2 to delete the atoms connected to the neighbors of those.
@@ -163,12 +163,12 @@ class ops_connected_Mixin:
             return
         
         alreadySelected = len(self.selatoms.values())
-        from op_select_doubly import select_doubly # new code, bruce 050520
+        from operations.op_select_doubly import select_doubly # new code, bruce 050520
         #e could also reload it now to speed devel!
         select_doubly(self.selatoms.values()) #e optim
         totalSelected = len(self.selatoms.values())
         
-        from PlatformDependent import fix_plurals
+        from platform.PlatformDependent import fix_plurals
         info = fix_plurals("%d new atom(s) selected (besides the %d initially selected)." % \
                                (totalSelected - alreadySelected, alreadySelected) )
         env.history.message( cmd + info)
diff --git a/cad/src/ops_copy.py b/cad/src/operations/ops_copy.py
index fb838cdf3..438a626cf 100755
--- a/cad/src/ops_copy.py
+++ b/cad/src/operations/ops_copy.py
@@ -14,18 +14,18 @@ bruce 050507 made this by collecting appropriate methods from class Part.
 from utilities import debug_flags
 import foundation.env as env
 
-from debug         import print_compact_stack
+from utilities.debug import print_compact_stack
 from utilities.Log import greenmsg, redmsg, orangemsg
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from foundation.Group import Group
 from model.chunk import Chunk
 from model.chunk import mol_copy_name
 from model.chem import Atom_prekill_prep
-from ops_select    import Selection
+from operations.ops_select import Selection
 from model.bonds import bond_copied_atoms
-from constants     import gensym
-from ops_select    import selection_from_part
-from constants     import noop
+from utilities.constants import gensym
+from operations.ops_select import selection_from_part
+from utilities.constants import noop
 from geometry.VQT import V
 from geometry.BoundingBox import BBox
 from model.jigs import Jig
@@ -167,9 +167,9 @@ class ops_copy_Mixin:
         # and emit message about what we're about to do
         if debug_flags.atom_debug: #bruce 050811 fixed this for A6 (it was a non-debug reload)
             print "atom_debug: fyi: importing or reloading ops_copy from itself"
-            import ops_copy as hmm
+            import operations.ops_copy as hmm
             reload(hmm)
-        from ops_copy import Copier # use latest code for that class, even if not for this mixin method!
+        from operations.ops_copy import Copier # use latest code for that class, even if not for this mixin method!
         copier = Copier(sel) #e sel.copier()?
         copier.prep_for_copy_to_shelf()
         if copier.objectsCopied == 0:  # wware 20051128, bug 1118, no error msg if already given
@@ -217,9 +217,9 @@ class ops_copy_Mixin:
         # and emit message about what we're about to do
         if debug_flags.atom_debug: #bruce 050811 fixed this for A6 (it was a non-debug reload)
             print "atom_debug: fyi: importing or reloading ops_copy from itself"
-            import ops_copy as hmm
+            import operations.ops_copy as hmm
             reload(hmm)
-        from ops_copy import Copier # use latest code for that class, even if not for this mixin method!
+        from operations.ops_copy import Copier # use latest code for that class, even if not for this mixin method!
         copier = Copier(sel) #e sel.copier()?
         copier.prep_for_copy_to_shelf()
         if copier.objectsCopied == 0:  # wware 20051128, bug 1118, no error msg if already given
@@ -266,9 +266,9 @@ class ops_copy_Mixin:
         sel = selection_from_part(entire_part, use_selatoms = True) #k use_selatoms is a guess
         if debug_flags.atom_debug:
             print "atom_debug: fyi: importing or reloading ops_copy from itself"
-            import ops_copy as hmm
+            import operations.ops_copy as hmm
             reload(hmm)
-        from ops_copy import Copier # use latest code for that class, even if not for this mixin method!
+        from operations.ops_copy import Copier # use latest code for that class, even if not for this mixin method!
         copier = Copier(sel) #e sel.copier()?
         copier.prep_for_copy_to_shelf() ###k guess: same prep method should be ok
         if copier.ok():
diff --git a/cad/src/ops_display.py b/cad/src/operations/ops_display.py
index 346ef64f0..6c30fdea6 100644
--- a/cad/src/ops_display.py
+++ b/cad/src/operations/ops_display.py
@@ -20,15 +20,15 @@ import foundation.env as env
 # Keep these in the same order that they are defined in constants.py.
 # It really helps since some lists are dependent on the display mode order.
 # Mark 2008-02-13.
-from constants import diDEFAULT
-from constants import diINVISIBLE
-from constants import diLINES
-from constants import diTUBES
-from constants import diBALL
-from constants import diTrueCPK
-from constants import diDNACYLINDER
-from constants import diCYLINDER
-from constants import diSURFACE
+from utilities.constants import diDEFAULT
+from utilities.constants import diINVISIBLE
+from utilities.constants import diLINES
+from utilities.constants import diTUBES
+from utilities.constants import diBALL
+from utilities.constants import diTrueCPK
+from utilities.constants import diDNACYLINDER
+from utilities.constants import diCYLINDER
+from utilities.constants import diSURFACE
 
 from PyQt4.Qt import Qt, QColorDialog, QColor
 
@@ -204,7 +204,7 @@ class displaySlotsMixin:
         
         _cmd = greenmsg("Change Color: ")
 
-        from ops_select import objectSelected, ATOMS, CHUNKS, JIGS
+        from operations.ops_select import objectSelected, ATOMS, CHUNKS, JIGS
         if not objectSelected(self.assy, objectFlags = CHUNKS | JIGS):
             if objectSelected(self.assy, objectFlags = ATOMS):
                 _msg = redmsg("Cannot change color of individual atoms.")
diff --git a/cad/src/ops_files.py b/cad/src/operations/ops_files.py
index f99b3afdc..8b558e0d8 100755
--- a/cad/src/ops_files.py
+++ b/cad/src/operations/ops_files.py
@@ -34,7 +34,7 @@ from PyQt4.Qt import QStringList
 import foundation.env as env
 from utilities import debug_flags
 
-from PlatformDependent import find_or_make_Nanorex_subdir
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
 
 from model.assembly import assembly
 
@@ -45,18 +45,18 @@ from graphics.rendering.fileIO import writepovfile
 from graphics.rendering.fileIO import writemdlfile
 from graphics.rendering.qutemol.qutemol import write_qutemol_pdb_file
 
-from debug import print_compact_traceback
-from debug import linenum
-from debug import begin_timing, end_timing
+from utilities.debug import print_compact_traceback
+from utilities.debug import linenum
+from utilities.debug import begin_timing, end_timing
 
 from utilities.Log import greenmsg, redmsg, orangemsg, _graymsg
 
-from prefs_constants import getDefaultWorkingDirectory
-from prefs_constants import workingDirectory_prefs_key
-from prefs_constants import toolbar_state_prefs_key
+from utilities.prefs_constants import getDefaultWorkingDirectory
+from utilities.prefs_constants import workingDirectory_prefs_key
+from utilities.prefs_constants import toolbar_state_prefs_key
 
-from debug_prefs import Choice_boolean_False
-from debug_prefs import debug_pref
+from utilities.debug_prefs import Choice_boolean_False
+from utilities.debug_prefs import debug_pref
 
 debug_babel = False   # DO NOT COMMIT with True
 
diff --git a/cad/src/ops_modify.py b/cad/src/operations/ops_modify.py
index 288731832..b2cbc1712 100644
--- a/cad/src/ops_modify.py
+++ b/cad/src/operations/ops_modify.py
@@ -4,7 +4,7 @@ ops_modify.py provides modifySlotsMixin for MWsemantics,
 with modify slot methods and related helper methods.
 
 @author: Mark
-@version: $Id:$
+@version: $Id$
 @copyright: 2008 Nanorex, Inc.  See LICENSE file for details.
 
 Note: most other ops_*.py files provide mixin classes for Part,
@@ -29,9 +29,9 @@ class modifySlotsMixin:
         """
         if debug_flags.atom_debug:
             print "debug: reloading runSim on each use, for development"
-            import runSim, debug
+            import simulation.runSim as runSim, utilities.debug as debug
             debug.reload_once_per_event(runSim)
-        from runSim import Minimize_CommandRun
+        from simulation.runSim import Minimize_CommandRun
         cmdrun = Minimize_CommandRun( self, 'Sel', type = 'Adjust')
         cmdrun.run()
         return
@@ -42,9 +42,9 @@ class modifySlotsMixin:
         """
         if debug_flags.atom_debug:
             print "debug: reloading runSim on each use, for development"
-            import runSim, debug
+            import simulation.runSim as runSim, utilities.debug as debug
             debug.reload_once_per_event(runSim)
-        from runSim import Minimize_CommandRun
+        from simulation.runSim import Minimize_CommandRun
         cmdrun = Minimize_CommandRun( self, 'All', type = 'Adjust')
         cmdrun.run()
         return
diff --git a/cad/src/ops_motion.py b/cad/src/operations/ops_motion.py
index 3079ac35c..a6ba62ba0 100755
--- a/cad/src/ops_motion.py
+++ b/cad/src/operations/ops_motion.py
@@ -13,11 +13,11 @@ bruce 050507 made this by collecting appropriate methods from class Part.
 """
 
 from utilities.Log import greenmsg, redmsg
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from geometry.VQT import V, norm, Q, vlen, orthodist
 import foundation.env as env
 from math import pi
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from model.chunk import Chunk
 from model.jigs import Jig
diff --git a/cad/src/ops_rechunk.py b/cad/src/operations/ops_rechunk.py
index 1337a4c3e..30a5c677e 100755
--- a/cad/src/ops_rechunk.py
+++ b/cad/src/operations/ops_rechunk.py
@@ -12,14 +12,14 @@ bruce 050507 made this by collecting appropriate methods from class Part.
 """
 
 from utilities.Log import greenmsg, redmsg
-from PlatformDependent import fix_plurals
+from platform.PlatformDependent import fix_plurals
 from model.chunk import Chunk
-from constants import gensym
+from utilities.constants import gensym
 from dna.model.Dna_Constants import getNextStrandColor
 import foundation.env as env
-from debug_prefs import debug_pref, Choice_boolean_False
-from debug import print_compact_stack
-from runSim import adjustSinglet
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
+from utilities.debug import print_compact_stack
+from simulation.runSim import adjustSinglet
 
 class ops_rechunk_Mixin:
     """
diff --git a/cad/src/ops_select.py b/cad/src/operations/ops_select.py
index 1f56e9b79..a9f15acc1 100755
--- a/cad/src/ops_select.py
+++ b/cad/src/operations/ops_select.py
@@ -11,8 +11,8 @@ History:
 bruce 050507 made this by collecting appropriate methods from class Part.
 """
 
-from constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
-from constants import diINVISIBLE, diDEFAULT
+from utilities.constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
+from utilities.constants import diINVISIBLE, diDEFAULT
 from model.jigs import Jig
 from model.chem import _changed_picked_Atoms
 from model.chunk import Chunk
@@ -21,11 +21,11 @@ from geometry.VQT import V, A, norm, cross
 from Numeric import dot, transpose
 import foundation.env as env
 from utilities.Log import redmsg, greenmsg, orangemsg
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 from utilities import debug_flags
-from PlatformDependent import fix_plurals
-from GlobalPreferences import permit_atom_chunk_coselection
-from icon_utilities import geticon
+from platform.PlatformDependent import fix_plurals
+from utilities.GlobalPreferences import permit_atom_chunk_coselection
+from utilities.icon_utilities import geticon
 
 from dna.model.DnaGroup import DnaGroup
 from cnt.model.CntGroup import CntGroup
diff --git a/cad/src/ops_view.py b/cad/src/operations/ops_view.py
index 1e51b40a0..a7e1fab0b 100755
--- a/cad/src/ops_view.py
+++ b/cad/src/operations/ops_view.py
@@ -20,8 +20,8 @@ from geometry.geometryUtilities import compute_heuristic_axis
 import foundation.env as env
 from geometry.VQT import V, Q, A, norm, vlen
 from utilities.Log import greenmsg, redmsg, orangemsg
-from prefs_constants import ORTHOGRAPHIC
-from prefs_constants import PERSPECTIVE
+from utilities.prefs_constants import ORTHOGRAPHIC
+from utilities.prefs_constants import PERSPECTIVE
 from model.NamedView import NamedView
 from model.PovrayScene import PovrayScene
 
diff --git a/cad/src/pastables.py b/cad/src/operations/pastables.py
index 7a94d0300..7a94d0300 100644
--- a/cad/src/pastables.py
+++ b/cad/src/operations/pastables.py
diff --git a/cad/src/reposition_baggage.py b/cad/src/operations/reposition_baggage.py
index 41634292c..41634292c 100755
--- a/cad/src/reposition_baggage.py
+++ b/cad/src/operations/reposition_baggage.py
diff --git a/cad/src/undo_UI.py b/cad/src/operations/undo_UI.py
index 43fe3089f..2e9e6c446 100644
--- a/cad/src/undo_UI.py
+++ b/cad/src/operations/undo_UI.py
@@ -20,7 +20,7 @@ out of undo_manager.py [as of 071025], so they may be misleadingly out of
 context.
 """
 
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 import foundation.env as env
 from utilities.Log import greenmsg, redmsg, _graymsg
diff --git a/cad/src/outtakes/MMKit.py b/cad/src/outtakes/MMKit.py
index 71b287a10..789e2e14e 100755
--- a/cad/src/outtakes/MMKit.py
+++ b/cad/src/outtakes/MMKit.py
@@ -37,7 +37,7 @@ from PyQt4.Qt import QDir, QTreeView, QTreeWidgetItem, QAbstractItemDelegate, QW
 from MMKitDialog import Ui_MMKitDialog
 from graphics.widgets.ThumbView import MMKitView, ChunkView
 from model.elements import PeriodicTable
-from constants import diTUBES
+from utilities.constants import diTUBES
 ## from chem import Atom [not used i think - bruce 071113]
 ## from chunk import Chunk [not used i think - bruce 071113]
 from foundation.Utility import imagename_to_icon, geticon
@@ -46,10 +46,10 @@ from files.mmp.files_mmp import readmmp
 from model.part import Part
 import foundation.env as env
 from utilities import debug_flags
-from debug import print_compact_traceback
-from Sponsors import SponsorableMixin
+from utilities.debug import print_compact_traceback
+from sponsors.Sponsors import SponsorableMixin
 from PropertyManagerMixin import PropertyManagerMixin, pmSetPropMgrIcon, pmSetPropMgrTitle
-from PropMgr_Constants import pmMMKitPageMargin
+from PM.PropMgr_Constants import pmMMKitPageMargin
 from model.bond_constants import btype_from_v6
 
 # PageId constants for mmkit_tab
@@ -189,7 +189,7 @@ class MMKit(QDialog,
         # adding a warning in the menu text, and adding a try/except to help in debugging this if anyone ever wants to.
         # (If the bugs Will mentioned go away entirely, we can abandon support for the False value instead of fixing it,
         #  as Will suggested.)
-        from debug_prefs import debug_pref, Choice_boolean_True
+        from utilities.debug_prefs import debug_pref, Choice_boolean_True
         self.icon_tabs = debug_pref("use icons in MMKit tabs? (only True works in Qt4)", Choice_boolean_True,
                                     prefs_key = "A7/mmkit tab icons/Qt4")
             #e Changes to this only take effect in the next session.
@@ -1010,7 +1010,7 @@ class MMKit(QDialog,
        if self.w.assy.filename: 
            odir = os.path.dirname(self.w.assy.filename)
        else: 
-           from prefs_constants import workingDirectory_prefs_key
+           from utilities.prefs_constants import workingDirectory_prefs_key
            odir = env.prefs[workingDirectory_prefs_key]
         
        fdir = QFileDialog.getExistingDirectory(self, "Choose library directory", odir)
diff --git a/cad/src/outtakes/MMKitDialog.py b/cad/src/outtakes/MMKitDialog.py
index 1fdb04ab3..76121d2d0 100755
--- a/cad/src/outtakes/MMKitDialog.py
+++ b/cad/src/outtakes/MMKitDialog.py
@@ -48,31 +48,31 @@ from PropertyManagerMixin import pmAddTopRowButtons
 from PropertyManagerMixin import pmMessageGroupBox
 from PropertyManagerMixin import pmAddBottomSpacer
 
-from PropMgr_Constants import pmDoneButton
-from PropMgr_Constants import pmWhatsThisButton
-from PropMgr_Constants import pmMainVboxLayoutMargin
-from PropMgr_Constants import pmMainVboxLayoutSpacing
-from PropMgr_Constants import pmHeaderFrameMargin
-from PropMgr_Constants import pmHeaderFrameSpacing
-from PropMgr_Constants import getHeaderFont
-from PropMgr_Constants import pmLabelLeftAlignment
-from PropMgr_Constants import pmSponsorFrameMargin
-from PropMgr_Constants import pmSponsorFrameSpacing
-from PropMgr_Constants import pmGroupBoxSpacing
-from PropMgr_Constants import pmTopRowBtnsMargin
-from PropMgr_Constants import pmTopRowBtnsSpacing
-from PropMgr_Constants import pmMessageTextEditColor
-from PropMgr_Constants import pmGrpBoxVboxLayoutMargin
-from PropMgr_Constants import pmGrpBoxVboxLayoutSpacing
-from PropMgr_Constants import pmMMKitPageMargin
-from PropMgr_Constants import pmMMKitButtonFont
-from PropMgr_Constants import pmMMKitButtonFontPointSize
-from PropMgr_Constants import pmMMKitButtonFontBold
-from PropMgr_Constants import pmMMKitButtonHeight
-from PropMgr_Constants import pmMMKitButtonWidth
-from prefs_constants import buildModeAutobondEnabled_prefs_key
-from prefs_constants import buildModeHighlightingEnabled_prefs_key
-from prefs_constants import buildModeWaterEnabled_prefs_key
+from PM.PropMgr_Constants import pmDoneButton
+from PM.PropMgr_Constants import pmWhatsThisButton
+from PM.PropMgr_Constants import pmMainVboxLayoutMargin
+from PM.PropMgr_Constants import pmMainVboxLayoutSpacing
+from PM.PropMgr_Constants import pmHeaderFrameMargin
+from PM.PropMgr_Constants import pmHeaderFrameSpacing
+from PM.PropMgr_Constants import getHeaderFont
+from PM.PropMgr_Constants import pmLabelLeftAlignment
+from PM.PropMgr_Constants import pmSponsorFrameMargin
+from PM.PropMgr_Constants import pmSponsorFrameSpacing
+from PM.PropMgr_Constants import pmGroupBoxSpacing
+from PM.PropMgr_Constants import pmTopRowBtnsMargin
+from PM.PropMgr_Constants import pmTopRowBtnsSpacing
+from PM.PropMgr_Constants import pmMessageTextEditColor
+from PM.PropMgr_Constants import pmGrpBoxVboxLayoutMargin
+from PM.PropMgr_Constants import pmGrpBoxVboxLayoutSpacing
+from PM.PropMgr_Constants import pmMMKitPageMargin
+from PM.PropMgr_Constants import pmMMKitButtonFont
+from PM.PropMgr_Constants import pmMMKitButtonFontPointSize
+from PM.PropMgr_Constants import pmMMKitButtonFontBold
+from PM.PropMgr_Constants import pmMMKitButtonHeight
+from PM.PropMgr_Constants import pmMMKitButtonWidth
+from utilities.prefs_constants import buildModeAutobondEnabled_prefs_key
+from utilities.prefs_constants import buildModeHighlightingEnabled_prefs_key
+from utilities.prefs_constants import buildModeWaterEnabled_prefs_key
         
 class Ui_MMKitDialog(object):
     """
diff --git a/cad/src/outtakes/PropMgrBaseClass.py b/cad/src/outtakes/PropMgrBaseClass.py
index d15c0ef86..f7627efbe 100755
--- a/cad/src/outtakes/PropMgrBaseClass.py
+++ b/cad/src/outtakes/PropMgrBaseClass.py
@@ -75,47 +75,47 @@ from PyQt4.Qt import QTextCursor
 
 from utilities import debug_flags
 
-from icon_utilities import geticon, getpixmap
-from debug import print_compact_traceback
-
-from PropMgr_Constants import pmColor
-from PropMgr_Constants import pmTitleFrameColor
-from PropMgr_Constants import pmTitleLabelColor
-from PropMgr_Constants import pmMinWidth
-from PropMgr_Constants import pmDefaultWidth
-from PropMgr_Constants import pmLabelRightAlignment
-from PropMgr_Constants import pmLabelLeftAlignment
-from PropMgr_Constants import pmMainVboxLayoutMargin
-from PropMgr_Constants import pmMainVboxLayoutSpacing
-from PropMgr_Constants import pmHeaderFrameMargin
-from PropMgr_Constants import pmHeaderFrameSpacing
-from PropMgr_Constants import getHeaderFont
-from PropMgr_Constants import pmSponsorFrameMargin
-from PropMgr_Constants import pmSponsorFrameSpacing
-from PropMgr_Constants import pmTopRowBtnsMargin
-from PropMgr_Constants import pmTopRowBtnsSpacing
-from PropMgr_Constants import pmGroupBoxSpacing
-from PropMgr_Constants import pmGrpBoxVboxLayoutMargin
-from PropMgr_Constants import pmGrpBoxVboxLayoutSpacing
-from PropMgr_Constants import pmGridLayoutMargin
-from PropMgr_Constants import pmGridLayoutSpacing
-from PropMgr_Constants import pmGrpBoxButtonColor
-from PropMgr_Constants import pmGrpBoxButtonBorderColor
-from PropMgr_Constants import pmGrpBoxButtonTextColor
-from PropMgr_Constants import pmGrpBoxExpandedImage
-from PropMgr_Constants import pmGrpBoxCollapsedImage
-from PropMgr_Constants import pmGrpBoxGridLayoutMargin
-from PropMgr_Constants import pmGrpBoxGridLayoutSpacing
-from PropMgr_Constants import pmGrpBoxColor
-from PropMgr_Constants import pmGrpBoxBorderColor
-from PropMgr_Constants import pmMsgGrpBoxMargin
-from PropMgr_Constants import pmMsgGrpBoxSpacing
-from PropMgr_Constants import pmMessageTextEditColor
-from PropMgr_Constants import pmDoneButton
-from PropMgr_Constants import pmCancelButton
-from PropMgr_Constants import pmRestoreDefaultsButton
-from PropMgr_Constants import pmPreviewButton
-from PropMgr_Constants import pmWhatsThisButton
+from utilities.icon_utilities import geticon, getpixmap
+from utilities.debug import print_compact_traceback
+
+from PM.PropMgr_Constants import pmColor
+from PM.PropMgr_Constants import pmTitleFrameColor
+from PM.PropMgr_Constants import pmTitleLabelColor
+from PM.PropMgr_Constants import pmMinWidth
+from PM.PropMgr_Constants import pmDefaultWidth
+from PM.PropMgr_Constants import pmLabelRightAlignment
+from PM.PropMgr_Constants import pmLabelLeftAlignment
+from PM.PropMgr_Constants import pmMainVboxLayoutMargin
+from PM.PropMgr_Constants import pmMainVboxLayoutSpacing
+from PM.PropMgr_Constants import pmHeaderFrameMargin
+from PM.PropMgr_Constants import pmHeaderFrameSpacing
+from PM.PropMgr_Constants import getHeaderFont
+from PM.PropMgr_Constants import pmSponsorFrameMargin
+from PM.PropMgr_Constants import pmSponsorFrameSpacing
+from PM.PropMgr_Constants import pmTopRowBtnsMargin
+from PM.PropMgr_Constants import pmTopRowBtnsSpacing
+from PM.PropMgr_Constants import pmGroupBoxSpacing
+from PM.PropMgr_Constants import pmGrpBoxVboxLayoutMargin
+from PM.PropMgr_Constants import pmGrpBoxVboxLayoutSpacing
+from PM.PropMgr_Constants import pmGridLayoutMargin
+from PM.PropMgr_Constants import pmGridLayoutSpacing
+from PM.PropMgr_Constants import pmGrpBoxButtonColor
+from PM.PropMgr_Constants import pmGrpBoxButtonBorderColor
+from PM.PropMgr_Constants import pmGrpBoxButtonTextColor
+from PM.PropMgr_Constants import pmGrpBoxExpandedImage
+from PM.PropMgr_Constants import pmGrpBoxCollapsedImage
+from PM.PropMgr_Constants import pmGrpBoxGridLayoutMargin
+from PM.PropMgr_Constants import pmGrpBoxGridLayoutSpacing
+from PM.PropMgr_Constants import pmGrpBoxColor
+from PM.PropMgr_Constants import pmGrpBoxBorderColor
+from PM.PropMgr_Constants import pmMsgGrpBoxMargin
+from PM.PropMgr_Constants import pmMsgGrpBoxSpacing
+from PM.PropMgr_Constants import pmMessageTextEditColor
+from PM.PropMgr_Constants import pmDoneButton
+from PM.PropMgr_Constants import pmCancelButton
+from PM.PropMgr_Constants import pmRestoreDefaultsButton
+from PM.PropMgr_Constants import pmPreviewButton
+from PM.PropMgr_Constants import pmWhatsThisButton
 
 # Special Qt debugging functions written by Mark. 2007-05-24 ############
 
diff --git a/cad/src/outtakes/PropertyManagerMixin.py b/cad/src/outtakes/PropertyManagerMixin.py
index 75b6c5eee..06d32a0dd 100755
--- a/cad/src/outtakes/PropertyManagerMixin.py
+++ b/cad/src/outtakes/PropertyManagerMixin.py
@@ -38,46 +38,46 @@ from PyQt4.Qt import QTextEdit
 
 from utilities import debug_flags
 
-from icon_utilities import geticon, getpixmap
-from Sponsors import SponsorableMixin
-from qt4transition import lineage
-from debug import print_compact_traceback
+from utilities.icon_utilities import geticon, getpixmap
+from sponsors.Sponsors import SponsorableMixin
+from utilities.qt4transition import lineage
+from utilities.debug import print_compact_traceback
 from PropMgrBaseClass import PropertyManager_common, getPalette
-from PropMgr_Constants import pmColor
-from PropMgr_Constants import pmAllButtons
-from PropMgr_Constants import pmTitleFrameColor
-from PropMgr_Constants import pmTitleLabelColor
-from PropMgr_Constants import pmMessageTextEditColor
-from PropMgr_Constants import pmGrpBoxColor
-from PropMgr_Constants import pmGrpBoxButtonColor
-from PropMgr_Constants import pmCheckBoxTextColor
-from PropMgr_Constants import pmCheckBoxButtonColor
-from PropMgr_Constants import pmGrpBoxBorderColor
-from PropMgr_Constants import pmGrpBoxButtonBorderColor
-from PropMgr_Constants import pmGrpBoxButtonTextColor
-from PropMgr_Constants import pmGrpBoxExpandedImage
-from PropMgr_Constants import pmGrpBoxCollapsedImage
-from PropMgr_Constants import pmGrpBoxVboxLayoutMargin
-from PropMgr_Constants import pmGrpBoxVboxLayoutSpacing
-from PropMgr_Constants import pmMainVboxLayoutMargin
-from PropMgr_Constants import pmMainVboxLayoutSpacing
-from PropMgr_Constants import pmHeaderFrameMargin
-from PropMgr_Constants import pmHeaderFrameSpacing
-from PropMgr_Constants import pmLabelLeftAlignment
-from PropMgr_Constants import getHeaderFont
-from PropMgr_Constants import pmSponsorFrameMargin
-from PropMgr_Constants import pmSponsorFrameSpacing
-from PropMgr_Constants import pmTopRowBtnsMargin
-from PropMgr_Constants import pmTopRowBtnsSpacing
-from PropMgr_Constants import pmDoneButton
-from PropMgr_Constants import pmCancelButton
-from PropMgr_Constants import pmRestoreDefaultsButton
-from PropMgr_Constants import pmPreviewButton
-from PropMgr_Constants import pmWhatsThisButton
-from PropMgr_Constants import pmMsgGrpBoxMargin
-from PropMgr_Constants import pmMsgGrpBoxSpacing
-from PropMgr_Constants import pmMinWidth
-from PropMgr_Constants import pmGroupBoxSpacing
+from PM.PropMgr_Constants import pmColor
+from PM.PropMgr_Constants import pmAllButtons
+from PM.PropMgr_Constants import pmTitleFrameColor
+from PM.PropMgr_Constants import pmTitleLabelColor
+from PM.PropMgr_Constants import pmMessageTextEditColor
+from PM.PropMgr_Constants import pmGrpBoxColor
+from PM.PropMgr_Constants import pmGrpBoxButtonColor
+from PM.PropMgr_Constants import pmCheckBoxTextColor
+from PM.PropMgr_Constants import pmCheckBoxButtonColor
+from PM.PropMgr_Constants import pmGrpBoxBorderColor
+from PM.PropMgr_Constants import pmGrpBoxButtonBorderColor
+from PM.PropMgr_Constants import pmGrpBoxButtonTextColor
+from PM.PropMgr_Constants import pmGrpBoxExpandedImage
+from PM.PropMgr_Constants import pmGrpBoxCollapsedImage
+from PM.PropMgr_Constants import pmGrpBoxVboxLayoutMargin
+from PM.PropMgr_Constants import pmGrpBoxVboxLayoutSpacing
+from PM.PropMgr_Constants import pmMainVboxLayoutMargin
+from PM.PropMgr_Constants import pmMainVboxLayoutSpacing
+from PM.PropMgr_Constants import pmHeaderFrameMargin
+from PM.PropMgr_Constants import pmHeaderFrameSpacing
+from PM.PropMgr_Constants import pmLabelLeftAlignment
+from PM.PropMgr_Constants import getHeaderFont
+from PM.PropMgr_Constants import pmSponsorFrameMargin
+from PM.PropMgr_Constants import pmSponsorFrameSpacing
+from PM.PropMgr_Constants import pmTopRowBtnsMargin
+from PM.PropMgr_Constants import pmTopRowBtnsSpacing
+from PM.PropMgr_Constants import pmDoneButton
+from PM.PropMgr_Constants import pmCancelButton
+from PM.PropMgr_Constants import pmRestoreDefaultsButton
+from PM.PropMgr_Constants import pmPreviewButton
+from PM.PropMgr_Constants import pmWhatsThisButton
+from PM.PropMgr_Constants import pmMsgGrpBoxMargin
+from PM.PropMgr_Constants import pmMsgGrpBoxSpacing
+from PM.PropMgr_Constants import pmMinWidth
+from PM.PropMgr_Constants import pmGroupBoxSpacing
 
 def pmVBoxLayout(propMgr):
     """Create the master vertical box layout for <propMgr>.
diff --git a/cad/src/outtakes/TreeWidget.py b/cad/src/outtakes/TreeWidget.py
index dc0ad92ca..c4835c391 100755
--- a/cad/src/outtakes/TreeWidget.py
+++ b/cad/src/outtakes/TreeWidget.py
@@ -20,9 +20,9 @@ and split it into three modules:
 assert 0, "TreeWidget.py is NO LONGER USED IN Qt4 NE1" #bruce 070503 Qt4
 
 from TreeView import * # including class TreeView, and import * from many other modules
-from menu_helpers import makemenu_helper
+from widgets.menu_helpers import makemenu_helper
 from platform import fix_buttons_helper
-from debug import DebugMenuMixin, print_compact_stack, print_compact_traceback
+from utilities.debug import DebugMenuMixin, print_compact_stack, print_compact_traceback
 allButtons = (leftButton|midButton|rightButton) #e should be defined in same file as the buttons
 from utilities import debug_flags
 from platform import tupleFromQPoint, fix_plurals
@@ -447,7 +447,7 @@ class TreeWidget(TreeView, DebugMenuMixin):
         would need to be separately passed anyway.)
         """
         if debug_flags.atom_debug: #bruce 060713 debug code, safe to be permanent
-            import debug
+            import utilities.debug as debug
             debug._event = event
             debug._event_state = event.state()
             debug._event_stateAfter = event.stateAfter()        
@@ -677,7 +677,7 @@ class TreeWidget(TreeView, DebugMenuMixin):
     def topmost_selected_nodes(self): #e might be needed by some context menus... how should the makers ask for it?
         "return a list of all selected nodes as seen by apply2picked, i.e. without looking inside selected Groups"
         #bruce 050523 revised this
-        from ops_select import topmost_selected_nodes
+        from operations.ops_select import topmost_selected_nodes
         return topmost_selected_nodes( self.topnodes)
 
     # selection logic
diff --git a/cad/src/outtakes/old_extrude_widgets.py b/cad/src/outtakes/old_extrude_widgets.py
index b3cc18bc2..20454dbdc 100644
--- a/cad/src/outtakes/old_extrude_widgets.py
+++ b/cad/src/outtakes/old_extrude_widgets.py
@@ -12,7 +12,7 @@ from PyQt4.Qt import QVBoxLayout
 from PyQt4.Qt import QHBoxLayout
 from PyQt4.Qt import QLabel
 
-from qt4transition import qt4warning, qt4todo
+from utilities.qt4transition import qt4warning, qt4todo
 
 # These don't exist in Qt4 but we can make begin(QVBox) and
 # begin(QHBox) act the same as before.
diff --git a/cad/src/outtakes/test_polyline_drag.py b/cad/src/outtakes/test_polyline_drag.py
index 91c180e03..e2bdd7ced 100644
--- a/cad/src/outtakes/test_polyline_drag.py
+++ b/cad/src/outtakes/test_polyline_drag.py
@@ -15,13 +15,13 @@ Just a stub for now.
 """
 __author__ = "bruce"
 
-from test_connectWithState import State_preMixin
+from prototype.test_connectWithState import State_preMixin
 
-from test_commands import ExampleCommand
+from prototype.test_commands import ExampleCommand
 
 from geometry.VQT import V
 
-from constants import red
+from utilities.constants import red
 
 # TODO: import the following from somewhere
 DX = V(1,0,0)
diff --git a/cad/src/outtakes/undo_related_timing_tests.py b/cad/src/outtakes/undo_related_timing_tests.py
index 8b367b4dc..8688d196b 100644
--- a/cad/src/outtakes/undo_related_timing_tests.py
+++ b/cad/src/outtakes/undo_related_timing_tests.py
@@ -8,16 +8,16 @@ $Id$
 # not all of these are needed, perhaps:
 from cPickle import dump, load, HIGHEST_PROTOCOL
 import foundation.env as env
-from debug import register_debug_menu_command, register_debug_menu_command_maker
+from utilities.debug import register_debug_menu_command, register_debug_menu_command_maker
     ###@@@ don't put all those commands in there -- use a submenu, use atom-debug,
     # or let them only show up if a related flag is set, or so...
 from PyQt4.Qt import SIGNAL, QObject, QWidget #k ok to do these imports at toplevel? I hope so, since we need them in several places.
-from constants import genKey, noop
+from utilities.constants import genKey, noop
 from utilities import debug_flags # for atom_debug [bruce 060128, suggested by Mark;
     # if this works, we should simplify some defs which worry if it's too early for this]
 
 
-from debug import call_func_with_timing_histmsg
+from utilities.debug import call_func_with_timing_histmsg
 
 def atpos_list(part):
     "Return a list of atom-position arrays, one per chunk in part. Warning: might include shared mutable arrays."
diff --git a/cad/src/outtakes/widget_hacks.py b/cad/src/outtakes/widget_hacks.py
index 745fa6d21..2dd32dc7e 100755
--- a/cad/src/outtakes/widget_hacks.py
+++ b/cad/src/outtakes/widget_hacks.py
@@ -93,7 +93,7 @@ def hack_QToolButton_1(qtoolbutton): #bruce 050729 experiment to work around QTo
         return # return early
     iconset = qtoolbutton.iconSet()
         ## Qt4 error: AttributeError: iconSet
-    from debug_prefs import modify_iconset_On_states
+    from utilities.debug_prefs import modify_iconset_On_states
     modify_iconset_On_states(iconset, use_color = toolbutton_highlight_color )
     qtoolbutton.setIcon(iconset) #k might not be needed
     return
diff --git a/cad/src/PlatformDependent.py b/cad/src/platform/PlatformDependent.py
index 6abe86485..246e7a196 100755
--- a/cad/src/PlatformDependent.py
+++ b/cad/src/platform/PlatformDependent.py
@@ -24,8 +24,8 @@ import sys, os, time
 from PyQt4.Qt import Qt, QDesktopWidget, QRect
 import foundation.env as env
 from utilities import debug_flags
-from debug import print_compact_traceback
-from debug import print_compact_stack
+from utilities.debug import print_compact_traceback
+from utilities.debug import print_compact_stack
 from utilities.Log import redmsg
 
 # == constants (or variables settable by a debugger) read by code in other modules
diff --git a/cad/src/platform/__init__.py b/cad/src/platform/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/platform/__init__.py
diff --git a/cad/src/gpl_only.py b/cad/src/platform/gpl_only.py
index 784f56b3e..784f56b3e 100755
--- a/cad/src/gpl_only.py
+++ b/cad/src/platform/gpl_only.py
diff --git a/cad/src/Plugins.py b/cad/src/processes/Plugins.py
index 965dc381d..72e272aa4 100644
--- a/cad/src/Plugins.py
+++ b/cad/src/processes/Plugins.py
@@ -23,7 +23,7 @@ the user maintain info needed to run external processes.
 import foundation.env as env
 import os
 from PyQt4.Qt import QMessageBox
-from Process import Process    
+from processes.Process import Process    
 
 def _dialogToOfferPluginPrefsFixup(caption, text):
     """
diff --git a/cad/src/Process.py b/cad/src/processes/Process.py
index 579f8603d..579f8603d 100755
--- a/cad/src/Process.py
+++ b/cad/src/processes/Process.py
diff --git a/cad/src/ServerManager.py b/cad/src/processes/ServerManager.py
index abf007d10..97e5127bb 100755
--- a/cad/src/ServerManager.py
+++ b/cad/src/processes/ServerManager.py
@@ -9,14 +9,14 @@ Unclear whether or not this is GAMESS-specific.
 @copyright: 2005-2007 Nanorex, Inc.  See LICENSE file for details. 
 """
 
-from ServerManagerDialog import Ui_ServerManagerDialog
+from processes.ServerManagerDialog import Ui_ServerManagerDialog
 from PyQt4.Qt import QDialog, QStringList, SIGNAL, QMessageBox
-from SimServer import SimServer
+from simulation.SimServer import SimServer
 import os
 import cPickle as pickle
-from debug import print_compact_stack
-from qt4transition import qt4todo
-from PlatformDependent import find_or_make_Nanorex_directory
+from utilities.debug import print_compact_stack
+from utilities.qt4transition import qt4todo
+from platform.PlatformDependent import find_or_make_Nanorex_directory
 
 class ServerManager(QDialog, Ui_ServerManagerDialog):
     """
diff --git a/cad/src/ServerManagerDialog.py b/cad/src/processes/ServerManagerDialog.py
index a40c7e955..a40c7e955 100755
--- a/cad/src/ServerManagerDialog.py
+++ b/cad/src/processes/ServerManagerDialog.py
diff --git a/cad/src/ServerManagerDialog.ui b/cad/src/processes/ServerManagerDialog.ui
index de1da2215..de1da2215 100755
--- a/cad/src/ServerManagerDialog.ui
+++ b/cad/src/processes/ServerManagerDialog.ui
diff --git a/cad/src/processes/__init__.py b/cad/src/processes/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/processes/__init__.py
diff --git a/cad/src/prototype/__init__.py b/cad/src/prototype/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/prototype/__init__.py
diff --git a/cad/src/example_expr_command.py b/cad/src/prototype/example_expr_command.py
index b7b231ed7..afec21a56 100644
--- a/cad/src/example_expr_command.py
+++ b/cad/src/prototype/example_expr_command.py
@@ -16,7 +16,7 @@ in which it was called ExampleCommand2E
 
 # == PM class
 
-from test_command_PMs import ExampleCommand2_PM
+from prototype.test_command_PMs import ExampleCommand2_PM
 
 from PM.PM_LineEdit      import PM_LineEdit
 from PM.PM_GroupBox      import PM_GroupBox
@@ -59,7 +59,7 @@ class ExampleCommand2E_PM( ExampleCommand2_PM ):
 # these imports are not needed in a minimal example like ExampleCommand2:
 
 from graphics.drawing.drawer import drawline
-from constants import red
+from utilities.constants import red
 from geometry.VQT import V
 from exprs.instance_helpers import get_glpane_InstanceHolder
 from exprs.draggable import DraggablyBoxed
@@ -73,7 +73,7 @@ class TextState(InstanceMacro): # rename?
     _value = TextRect(text) # need size?
     pass
 
-from test_commands import ExampleCommand2
+from prototype.test_commands import ExampleCommand2
 
 ##from selectAtomsMode import selectAtomsMode
 ##from commands.SelectAtoms.SelectAtoms_Command import SelectAtoms_Command # used indirectly via ExampleCommand2
diff --git a/cad/src/test_command_PMs.py b/cad/src/prototype/test_command_PMs.py
index 170c999ba..170c999ba 100755
--- a/cad/src/test_command_PMs.py
+++ b/cad/src/prototype/test_command_PMs.py
diff --git a/cad/src/test_commands.py b/cad/src/prototype/test_commands.py
index a6465545e..cb4d64330 100755
--- a/cad/src/test_commands.py
+++ b/cad/src/prototype/test_commands.py
@@ -40,8 +40,8 @@ When cleaning up PropMgrBaseClass etc, note some other things Mark wants to work
 Fix problems with Example_TemporaryCommand_useParentPM (commented where it's used)
 """
 
-from test_command_PMs import ExampleCommand1_PM
-from test_command_PMs import ExampleCommand2_PM
+from prototype.test_command_PMs import ExampleCommand1_PM
+from prototype.test_command_PMs import ExampleCommand2_PM
 
 from PM.PM_WidgetsDemoPropertyManager import PM_WidgetsDemoPropertyManager
 
diff --git a/cad/src/test_commands_init.py b/cad/src/prototype/test_commands_init.py
index 129d88b50..3b3293751 100755
--- a/cad/src/test_commands_init.py
+++ b/cad/src/prototype/test_commands_init.py
@@ -9,9 +9,9 @@ How to run these test commands: see test_commands.py docstring.
 This is initialized in startup_misc.py as of 071030.
 """
 
-from debug import register_debug_menu_command
+from utilities.debug import register_debug_menu_command
 
-import EndUser, Initialize
+import utilities.EndUser as EndUser, utilities.Initialize as Initialize
 
 # ==
 
@@ -74,18 +74,18 @@ def enter_example_command(widget, example_command_classname):
 
             glpane._reinit_modes() # try to avoid problems with changing to other modes later, caused by those reloads
                 # wrong: uses old classes from glpane
-        import test_command_PMs
+        import prototype.test_command_PMs as test_command_PMs
         reload(test_command_PMs)
         Initialize.forgetInitialization(__name__)
-        import test_commands_init
+        import prototype.test_commands_init as test_commands_init
         reload(test_commands_init)
         test_commands_init.initialize()
             # (note: reload code is untested since the change [bruce 071030]
             #  to call initialize explicitly rather than as import side effect,
             #  done together with splitting this module out of test_commands)
-        from test_commands_init import enter_example_command_doit
+        from prototype.test_commands_init import enter_example_command_doit
     else:
-        from test_commands_init import enter_example_command_doit
+        from prototype.test_commands_init import enter_example_command_doit
         
     enter_example_command_doit(glpane, example_command_classname)
     return
@@ -111,19 +111,19 @@ def initialize():
     classnames = [ ] # extended below
 
     global ExampleCommand1
-    from test_commands import ExampleCommand1
+    from prototype.test_commands import ExampleCommand1
     classnames.append("ExampleCommand1")
 
     global ExampleCommand2
-    from test_commands import ExampleCommand2
+    from prototype.test_commands import ExampleCommand2
     classnames.append("ExampleCommand2")
 
     global test_connectWithState
-    from test_connectWithState import test_connectWithState
+    from prototype.test_connectWithState import test_connectWithState
     classnames.append("test_connectWithState")
 
     global ExampleCommand2E
-    from example_expr_command import ExampleCommand2E
+    from prototype.example_expr_command import ExampleCommand2E
     classnames.append("ExampleCommand2E")
 
     for classname in classnames:
diff --git a/cad/src/test_connectWithState.py b/cad/src/prototype/test_connectWithState.py
index a07357d9e..8342cce2a 100644
--- a/cad/src/test_connectWithState.py
+++ b/cad/src/prototype/test_connectWithState.py
@@ -10,10 +10,10 @@ History:
 070830 bruce split this out of test_commands.py
 """
 
-from test_connectWithState_constants import CYLINDER_HEIGHT_PREFS_KEY, CYLINDER_HEIGHT_DEFAULT_VALUE
-from test_connectWithState_constants import cylinder_round_caps
+from prototype.test_connectWithState_constants import CYLINDER_HEIGHT_PREFS_KEY, CYLINDER_HEIGHT_DEFAULT_VALUE
+from prototype.test_connectWithState_constants import cylinder_round_caps
 ##from test_connectWithState_constants import CYLINDER_VERTICAL_DEFAULT_VALUE
-from test_connectWithState_constants import CYLINDER_WIDTH_DEFAULT_VALUE
+from prototype.test_connectWithState_constants import CYLINDER_WIDTH_DEFAULT_VALUE
     ### better to define here... ### REVISE
 
     ### REVISE: the default value should come from the stateref, when using the State macro,
@@ -46,17 +46,17 @@ def set_cylinder_height(val):
 
 # === PM class
 
-from test_connectWithState_PM import test_connectWithState_PM
+from prototype.test_connectWithState_PM import test_connectWithState_PM
 
 
 # === GraphicsMode and Command classes
 
-from test_commands import ExampleCommand
+from prototype.test_commands import ExampleCommand
 
 from geometry.VQT import V
 from geometry.VQT import cross
 
-from constants import pink, white
+from utilities.constants import pink, white
 # TODO: import the following from somewhere
 DX = V(1,0,0)
 DY = V(0,1,0)
@@ -75,7 +75,7 @@ from exprs.Rect import Rect # used to make our drag handle appearance
 from exprs.DraggableHandle import DraggableHandle_AlongLine
 from exprs.If_expr import If_expr
 
-from prefs_widgets import ObjAttr_StateRef
+from widgets.prefs_widgets import ObjAttr_StateRef
 
 class State_preMixin( IorE_guest_mixin):
     # TODO: refile (alongside IorE_guest_mixin ? in its own file?), once cleaned up & bugfixed --
diff --git a/cad/src/test_connectWithState_PM.py b/cad/src/prototype/test_connectWithState_PM.py
index 414ac698e..7f7f2bfa8 100644
--- a/cad/src/test_connectWithState_PM.py
+++ b/cad/src/prototype/test_connectWithState_PM.py
@@ -20,16 +20,16 @@ History:
 # and we'll also optimize the State macro and make it easier to use. 
 
 
-from prefs_widgets import Preferences_StateRef, Preferences_StateRef_double # TODO: remove these imports, get the refs from the model
+from widgets.prefs_widgets import Preferences_StateRef, Preferences_StateRef_double # TODO: remove these imports, get the refs from the model
 
-from prefs_widgets import ObjAttr_StateRef # TODO: shorter or clearer name -- attribute_ref ?
+from widgets.prefs_widgets import ObjAttr_StateRef # TODO: shorter or clearer name -- attribute_ref ?
 
-from test_connectWithState_constants import CYLINDER_HEIGHT_PREFS_KEY, CYLINDER_HEIGHT_DEFAULT_VALUE
-from test_connectWithState_constants import CYLINDER_ROUND_CAPS_PREFS_KEY, CYLINDER_ROUND_CAPS_DEFAULT_VALUE # TODO: get prefs refs from model so these are not needed here
+from prototype.test_connectWithState_constants import CYLINDER_HEIGHT_PREFS_KEY, CYLINDER_HEIGHT_DEFAULT_VALUE
+from prototype.test_connectWithState_constants import CYLINDER_ROUND_CAPS_PREFS_KEY, CYLINDER_ROUND_CAPS_DEFAULT_VALUE # TODO: get prefs refs from model so these are not needed here
 ##from test_connectWithState_constants import CYLINDER_VERTICAL_DEFAULT_VALUE
 ##from test_connectWithState_constants import CYLINDER_WIDTH_DEFAULT_VALUE
 
-from test_command_PMs import ExampleCommand1_PM
+from prototype.test_command_PMs import ExampleCommand1_PM
 
 from PM.PM_GroupBox      import PM_GroupBox
 from PM.PM_DoubleSpinBox import PM_DoubleSpinBox
diff --git a/cad/src/test_connectWithState_constants.py b/cad/src/prototype/test_connectWithState_constants.py
index ec73e9cf7..ec73e9cf7 100644
--- a/cad/src/test_connectWithState_constants.py
+++ b/cad/src/prototype/test_connectWithState_constants.py
diff --git a/cad/src/scratch/DirView.py b/cad/src/scratch/DirView.py
index e457f4e8f..580c3e43b 100755
--- a/cad/src/scratch/DirView.py
+++ b/cad/src/scratch/DirView.py
@@ -32,7 +32,7 @@ from PyQt4.Qt import QSize
 from PyQt4.Qt import QDir
 from PyQt4.Qt import QApplication
 
-from qt4transition import qt4todo
+from utilities.qt4transition import qt4todo
 
 folder_closed_image =[
     "16 16 9 1",
diff --git a/cad/src/scratch/api_enforcement.py b/cad/src/scratch/api_enforcement.py
index 168c20b50..29f7eb32c 100644
--- a/cad/src/scratch/api_enforcement.py
+++ b/cad/src/scratch/api_enforcement.py
@@ -18,7 +18,7 @@ Bruce 071107 split it from debug.py into this scratch file.
 # REVIEW: might require some imports from debug.py
 
 import sys, os, time, types, traceback
-from constants import noop
+from utilities.constants import noop
 import foundation.env as env
 from utilities import debug_flags
 
diff --git a/cad/src/scratch/canvas-b-3.py b/cad/src/scratch/canvas-b-3.py
index 0705ba3eb..e93deec5f 100755
--- a/cad/src/scratch/canvas-b-3.py
+++ b/cad/src/scratch/canvas-b-3.py
@@ -34,7 +34,7 @@ import random
 
 import time #bruce
 try:
-    from debug import print_compact_stack
+    from utilities.debug import print_compact_stack
 except:
     print "could not import print_compact_stack"
     def print_compact_stack(msg):
diff --git a/cad/src/GROMACS.py b/cad/src/simulation/GROMACS/GROMACS.py
index ebe193b0f..77a984dba 100755
--- a/cad/src/GROMACS.py
+++ b/cad/src/simulation/GROMACS/GROMACS.py
@@ -83,7 +83,7 @@ class GROMACS:
         # Create a unique directory under the Nanorex/SimFiles directory for our
         # files: Nanorex/SimFiles/GMX-<timestamp>
         #
-        from PlatformDependent import find_or_make_Nanorex_subdir
+        from platform.PlatformDependent import find_or_make_Nanorex_subdir
         simFilesPath = find_or_make_Nanorex_subdir('SimFiles')
         timestamp = datetime.today()
         self.tempFilePath = \
diff --git a/cad/src/simulation/GROMACS/__init__.py b/cad/src/simulation/GROMACS/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/simulation/GROMACS/__init__.py
diff --git a/cad/src/PyrexSimulator.py b/cad/src/simulation/PyrexSimulator.py
index 0fc794cbe..6817cc09a 100644
--- a/cad/src/PyrexSimulator.py
+++ b/cad/src/simulation/PyrexSimulator.py
@@ -11,7 +11,7 @@ src/sim/globals.c.
 
 import os
 import foundation.env as env
-from PlatformDependent import find_plugin_dir
+from platform.PlatformDependent import find_plugin_dir
 
 _thePyrexSimulator = None
 
diff --git a/cad/src/SimJob.py b/cad/src/simulation/SimJob.py
index 6b99bf641..6b99bf641 100755
--- a/cad/src/SimJob.py
+++ b/cad/src/simulation/SimJob.py
diff --git a/cad/src/SimServer.py b/cad/src/simulation/SimServer.py
index 40732cef9..40732cef9 100755
--- a/cad/src/SimServer.py
+++ b/cad/src/simulation/SimServer.py
diff --git a/cad/src/SimSetup.py b/cad/src/simulation/SimSetup.py
index 947c9bbda..3f89b135e 100755
--- a/cad/src/SimSetup.py
+++ b/cad/src/simulation/SimSetup.py
@@ -28,14 +28,14 @@ from PyQt4.Qt import SIGNAL
 
 import foundation.env as env
 
-from SimSetupDialog import Ui_SimSetupDialog
-from movie import Movie
-from debug import print_compact_traceback
-from prefs_widgets import connect_checkbox_with_boolean_pref
-from prefs_constants import Potential_energy_tracefile_prefs_key
-from prefs_constants import electrostaticsForDnaDuringDynamics_prefs_key
-from debug_prefs import debug_pref, Choice_boolean_False
-from qt4transition import qt4todo
+from simulation.SimSetupDialog import Ui_SimSetupDialog
+from simulation.movie import Movie
+from utilities.debug import print_compact_traceback
+from widgets.prefs_widgets import connect_checkbox_with_boolean_pref
+from utilities.prefs_constants import Potential_energy_tracefile_prefs_key
+from utilities.prefs_constants import electrostaticsForDnaDuringDynamics_prefs_key
+from utilities.debug_prefs import debug_pref, Choice_boolean_False
+from utilities.qt4transition import qt4todo
 
 # class FakeMovie:
 #
@@ -170,7 +170,7 @@ class SimSetup(QDialog, Ui_SimSetupDialog): # before 050325 this class was calle
 
         try:
             #bruce 060705 use new common code, if it works
-            from widget_controllers import realtime_update_controller
+            from widgets.widget_controllers import realtime_update_controller
             self.ruc = realtime_update_controller(
                 ( self.update_btngrp_group, self.update_number_spinbox, self.update_units_combobox ),
                 self.watch_motion_checkbox
@@ -205,7 +205,7 @@ class SimSetup(QDialog, Ui_SimSetupDialog): # before 050325 this class was calle
             #
             # Brian Helfrich 2007-04-06
             #
-            from GROMACS import GROMACS
+            from simulation.GROMACS.GROMACS import GROMACS
             gmx = GROMACS(self.assy.part)
             gmx.run("md")
 
diff --git a/cad/src/SimSetupDialog.py b/cad/src/simulation/SimSetupDialog.py
index 602bfab63..602bfab63 100755
--- a/cad/src/SimSetupDialog.py
+++ b/cad/src/simulation/SimSetupDialog.py
diff --git a/cad/src/SimSetupDialog.ui b/cad/src/simulation/SimSetupDialog.ui
index 07250fe47..07250fe47 100755
--- a/cad/src/SimSetupDialog.ui
+++ b/cad/src/simulation/SimSetupDialog.ui
diff --git a/cad/src/simulation/__init__.py b/cad/src/simulation/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/simulation/__init__.py
diff --git a/cad/src/movie.py b/cad/src/simulation/movie.py
index a22aedbac..2973957b1 100755
--- a/cad/src/movie.py
+++ b/cad/src/simulation/movie.py
@@ -20,8 +20,8 @@ from utilities.Log import redmsg, orangemsg, greenmsg
 from geometry.VQT import A
 from model.chem import move_alist_and_snuggle
 from utilities import debug_flags
-from PlatformDependent import fix_plurals
-from debug import print_compact_stack, print_compact_traceback
+from platform.PlatformDependent import fix_plurals
+from utilities.debug import print_compact_stack, print_compact_traceback
 from files.dpb_trajectory.moviefile import MovieFile #e might be renamed, creation API revised, etc
 
 import foundation.env as env
diff --git a/cad/src/runSim.py b/cad/src/simulation/runSim.py
index a5e7ebcb2..7218cb497 100755
--- a/cad/src/runSim.py
+++ b/cad/src/simulation/runSim.py
@@ -27,24 +27,24 @@ simulator executable command-line flag is hardcoded.
 bruce 051231 partly-done code for using pyrex interface to sim; see use_dylib
 """
 
-from debug import print_compact_traceback
-import DebugMenuMixin
+from utilities.debug import print_compact_traceback
+import widgets.DebugMenuMixin as DebugMenuMixin
 #from DebugMenuMixin import sim_params_set # DebugMenuMixin needs refactoring
     # to move this variable (sim_params_set) (and related code?) out of it;
     # see its module docstring for more info [bruce 080104 comment]
 from utilities import debug_flags
-from PlatformDependent import fix_plurals
-from PlatformDependent import find_or_make_Nanorex_subdir
-from PlatformDependent import hhmmss_str
-from PlatformDependent import find_plugin_dir
+from platform.PlatformDependent import fix_plurals
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
+from platform.PlatformDependent import hhmmss_str
+from platform.PlatformDependent import find_plugin_dir
 import os, sys, time
 from math import sqrt
 from time import sleep
 from datetime import datetime
-from SimSetup import SimSetup
+from simulation.SimSetup import SimSetup
 from PyQt4.Qt import QApplication, QCursor, Qt, QStringList
 from PyQt4.Qt import QProcess, QObject, QFileInfo, SIGNAL
-from movie import Movie
+from simulation.movie import Movie
 from utilities.Log import redmsg, greenmsg, orangemsg, quote_html, _graymsg
 import foundation.env as env
 from foundation.env import seen_before
@@ -52,26 +52,26 @@ from geometry.VQT import A
 import re
 from model.chem import AtomDict
 from model.chunk import Chunk
-from debug_prefs import debug_pref, Choice, Choice_boolean_True, Choice_boolean_False
-from constants import filesplit
-from Process import Process
-from Plugins import checkPluginPreferences
-from StatusBar import AbortHandler, FileSizeProgressReporter
-from PyrexSimulator import thePyrexSimulator
-
-from prefs_constants import electrostaticsForDnaDuringAdjust_prefs_key
-from prefs_constants import electrostaticsForDnaDuringMinimize_prefs_key
-from prefs_constants import electrostaticsForDnaDuringDynamics_prefs_key
-from prefs_constants import Adjust_minimizationEngine_prefs_key
-
-from prefs_constants import gromacs_enabled_prefs_key
-from prefs_constants import gromacs_path_prefs_key
-from prefs_constants import cpp_enabled_prefs_key
-from prefs_constants import cpp_path_prefs_key
-
-from prefs_constants import MINIMIZE_ENGINE_UNSPECIFIED
-from prefs_constants import MINIMIZE_ENGINE_GROMACS_FOREGROUND
-from prefs_constants import MINIMIZE_ENGINE_GROMACS_BACKGROUND
+from utilities.debug_prefs import debug_pref, Choice, Choice_boolean_True, Choice_boolean_False
+from utilities.constants import filesplit
+from processes.Process import Process
+from processes.Plugins import checkPluginPreferences
+from widgets.StatusBar import AbortHandler, FileSizeProgressReporter
+from simulation.PyrexSimulator import thePyrexSimulator
+
+from utilities.prefs_constants import electrostaticsForDnaDuringAdjust_prefs_key
+from utilities.prefs_constants import electrostaticsForDnaDuringMinimize_prefs_key
+from utilities.prefs_constants import electrostaticsForDnaDuringDynamics_prefs_key
+from utilities.prefs_constants import Adjust_minimizationEngine_prefs_key
+
+from utilities.prefs_constants import gromacs_enabled_prefs_key
+from utilities.prefs_constants import gromacs_path_prefs_key
+from utilities.prefs_constants import cpp_enabled_prefs_key
+from utilities.prefs_constants import cpp_path_prefs_key
+
+from utilities.prefs_constants import MINIMIZE_ENGINE_UNSPECIFIED
+from utilities.prefs_constants import MINIMIZE_ENGINE_GROMACS_FOREGROUND
+from utilities.prefs_constants import MINIMIZE_ENGINE_GROMACS_BACKGROUND
 
 # more imports lower down
 
@@ -1005,10 +1005,10 @@ class SimRunner:
             # we'll probably use different prefs keys depending on an arg that tells us which command-class to use,
             # Adjust, Minimize, or Adjust Atoms; maybe some function in prefs_constants will return the prefs_key,
             # so all the UI code can call it too. [bruce 060705]
-            from prefs_constants import Adjust_endRMS_prefs_key, Adjust_endMax_prefs_key
-            from prefs_constants import Adjust_cutoverRMS_prefs_key, Adjust_cutoverMax_prefs_key
-            from prefs_constants import Minimize_endRMS_prefs_key, Minimize_endMax_prefs_key
-            from prefs_constants import Minimize_cutoverRMS_prefs_key, Minimize_cutoverMax_prefs_key
+            from utilities.prefs_constants import Adjust_endRMS_prefs_key, Adjust_endMax_prefs_key
+            from utilities.prefs_constants import Adjust_cutoverRMS_prefs_key, Adjust_cutoverMax_prefs_key
+            from utilities.prefs_constants import Minimize_endRMS_prefs_key, Minimize_endMax_prefs_key
+            from utilities.prefs_constants import Minimize_cutoverRMS_prefs_key, Minimize_cutoverMax_prefs_key
 
             # kluge for A8 -- ideally these prefs keys or their prefs values
             # would be set as movie object attrs like all other sim params
@@ -2401,7 +2401,7 @@ class Minimize_CommandRun(CommandRun):
                 env.history.message( msg)
                 return
         elif cmdtype == LOCAL_MIN:
-            from ops_select import selection_from_atomlist
+            from operations.ops_select import selection_from_atomlist
             junk, atomlist, ntimes_expand = self.args
             selection = selection_from_atomlist( self.part, atomlist) #e in cleaned up code, selection object might come from outside
             selection.expand_atomset(ntimes = ntimes_expand) # ok if ntimes == 0
@@ -2592,9 +2592,9 @@ class Minimize_CommandRun(CommandRun):
             # Just get the values from the General Prefs page.
             # But at least try to do that using new common code.
             try:
-                from widget_controllers import realtime_update_controller
+                from widgets.widget_controllers import realtime_update_controller
                 userPrefs = env.mainwindow().userPrefs
-                from prefs_constants import Adjust_watchRealtimeMinimization_prefs_key ###@@@ should depend on command, or be in movie...
+                from utilities.prefs_constants import Adjust_watchRealtimeMinimization_prefs_key ###@@@ should depend on command, or be in movie...
                 ruc = realtime_update_controller(
                     ( userPrefs.update_btngrp_group, ###k name
                       userPrefs.update_number_spinbox, userPrefs.update_units_combobox ),
diff --git a/cad/src/Sponsors.py b/cad/src/sponsors/Sponsors.py
index add8436dd..a9209a5b3 100755
--- a/cad/src/Sponsors.py
+++ b/cad/src/sponsors/Sponsors.py
@@ -55,15 +55,15 @@ from PyQt4.Qt import SIGNAL
 import foundation.env as env
 from utilities import debug_flags
 
-from PlatformDependent import find_or_make_Nanorex_subdir
+from platform.PlatformDependent import find_or_make_Nanorex_subdir
 from foundation.wiki_help import WikiHelpBrowser
-from debug import print_compact_stack, print_compact_traceback
-from qt4transition import qt4todo
-from prefs_constants import sponsor_download_permission_prefs_key
-from prefs_constants import sponsor_permanent_permission_prefs_key
-from prefs_constants import sponsor_md5_mismatch_flag_key
+from utilities.debug import print_compact_stack, print_compact_traceback
+from utilities.qt4transition import qt4todo
+from utilities.prefs_constants import sponsor_download_permission_prefs_key
+from utilities.prefs_constants import sponsor_permanent_permission_prefs_key
+from utilities.prefs_constants import sponsor_md5_mismatch_flag_key
 from utilities.Log import redmsg, orangemsg, greenmsg
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 _sponsordir = find_or_make_Nanorex_subdir('Sponsors')
 _sponsors = { }
diff --git a/cad/src/sponsors/__init__.py b/cad/src/sponsors/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/sponsors/__init__.py
diff --git a/cad/src/sponsors.xml b/cad/src/sponsors/sponsors.xml
index 411fe3f43..411fe3f43 100755
--- a/cad/src/sponsors.xml
+++ b/cad/src/sponsors/sponsors.xml
diff --git a/cad/src/LineMode.py b/cad/src/temporary_commands/LineMode.py
index 349c3ddeb..120e2fcb0 100644
--- a/cad/src/LineMode.py
+++ b/cad/src/temporary_commands/LineMode.py
@@ -22,7 +22,7 @@ from commands.Select.Select_Command import Select_Command
 from commands.Select.Select_GraphicsMode import Select_GraphicsMode
 
 from graphics.drawing.drawer import drawline, drawsphere
-from constants import black, darkred, blue
+from utilities.constants import black, darkred, blue
 
 from geometry.VQT import vlen, norm, angleBetween, V, ptonline
 
diff --git a/cad/src/PanMode.py b/cad/src/temporary_commands/PanMode.py
index ac145f8e4..e900e46a7 100755
--- a/cad/src/PanMode.py
+++ b/cad/src/temporary_commands/PanMode.py
@@ -8,7 +8,7 @@ Pan mode functionality.
 @license:   GPL
 """
 
-from TemporaryCommand import TemporaryCommand_Overdrawing
+from temporary_commands.TemporaryCommand import TemporaryCommand_Overdrawing
 
 # == GraphicsMode part
 
diff --git a/cad/src/RotateMode.py b/cad/src/temporary_commands/RotateMode.py
index 238f3be4c..f4d113f9e 100755
--- a/cad/src/RotateMode.py
+++ b/cad/src/temporary_commands/RotateMode.py
@@ -8,7 +8,7 @@ Rotate mode functionality.
 @license:   GPL
 """
 
-from TemporaryCommand import TemporaryCommand_Overdrawing
+from temporary_commands.TemporaryCommand import TemporaryCommand_Overdrawing
 
 # == GraphicsMode part
 
diff --git a/cad/src/TemporaryCommand.py b/cad/src/temporary_commands/TemporaryCommand.py
index 18fe454df..18fe454df 100644
--- a/cad/src/TemporaryCommand.py
+++ b/cad/src/temporary_commands/TemporaryCommand.py
diff --git a/cad/src/ZoomInOutMode.py b/cad/src/temporary_commands/ZoomInOutMode.py
index b90d3e6ee..5dcf83c3e 100644
--- a/cad/src/ZoomInOutMode.py
+++ b/cad/src/temporary_commands/ZoomInOutMode.py
@@ -9,7 +9,7 @@ Zoom in/out mode functionality.
 """
 
 from Numeric import exp
-from TemporaryCommand import TemporaryCommand_Overdrawing
+from temporary_commands.TemporaryCommand import TemporaryCommand_Overdrawing
 
 # == GraphicsMode part
 
diff --git a/cad/src/ZoomToAreaMode.py b/cad/src/temporary_commands/ZoomToAreaMode.py
index 41c060a54..654de921b 100755
--- a/cad/src/ZoomToAreaMode.py
+++ b/cad/src/temporary_commands/ZoomToAreaMode.py
@@ -29,10 +29,10 @@ from OpenGL.GLU import gluUnProject
 
 from geometry.VQT import V, A
 import graphics.drawing.drawer as drawer
-from constants import GL_FAR_Z
+from utilities.constants import GL_FAR_Z
 
 
-from TemporaryCommand import TemporaryCommand_Overdrawing
+from temporary_commands.TemporaryCommand import TemporaryCommand_Overdrawing
 
 
 # == the GraphicsMode part
diff --git a/cad/src/temporary_commands/__init__.py b/cad/src/temporary_commands/__init__.py
new file mode 100644
index 000000000..e69de29bb
--- /dev/null
+++ b/cad/src/temporary_commands/__init__.py
diff --git a/cad/src/EndUser.py b/cad/src/utilities/EndUser.py
index d046b6ed2..d046b6ed2 100755
--- a/cad/src/EndUser.py
+++ b/cad/src/utilities/EndUser.py
diff --git a/cad/src/GlobalPreferences.py b/cad/src/utilities/GlobalPreferences.py
index d084e3fce..999822680 100644
--- a/cad/src/GlobalPreferences.py
+++ b/cad/src/utilities/GlobalPreferences.py
@@ -15,9 +15,9 @@ the kinds of things in it so far -- bruce 080220 comment]
 @copyright: 2006-2008 Nanorex, Inc.  See LICENSE file for details.
 """
 
-from prefs_constants import permit_atom_chunk_coselection_prefs_key
-from debug_prefs import debug_pref, Choice_boolean_False ##, Choice_boolean_True
-from debug import print_compact_traceback
+from utilities.prefs_constants import permit_atom_chunk_coselection_prefs_key
+from utilities.debug_prefs import debug_pref, Choice_boolean_False ##, Choice_boolean_True
+from utilities.debug import print_compact_traceback
 
 # ==
 
diff --git a/cad/src/Initialize.py b/cad/src/utilities/Initialize.py
index 9a816af42..9a816af42 100755
--- a/cad/src/Initialize.py
+++ b/cad/src/utilities/Initialize.py
diff --git a/cad/src/constants.py b/cad/src/utilities/constants.py
index 503368568..16db3e64b 100755
--- a/cad/src/constants.py
+++ b/cad/src/utilities/constants.py
@@ -411,11 +411,8 @@ except:
 else:
     import os
     CAD_SRC_PATH = os.path.dirname(__file__)
-    assert not CAD_SRC_PATH.endswith("utilities") # this will fail if we
-        # forget to fix this definition when moving this file into the
-        # utilities package. When we do, activate the following code:
-        ## assert os.path.basename(CAD_SRC_PATH) == "utilities"
-        ## CAD_SRC_PATH = os.path.dirname(CAD_SRC_PATH)
+    assert os.path.basename(CAD_SRC_PATH) == "utilities"
+    CAD_SRC_PATH = os.path.dirname(CAD_SRC_PATH)
     #print "CAD_SRC_PATH = %r" % CAD_SRC_PATH ### REMOVE WHEN WORKS, BEFORE COMMIT
     # [review: in a built Mac release, CAD_SRC_PATH might be
     # .../Contents/Resources/Python/site-packages.zip, or a related pathname
diff --git a/cad/src/debug.py b/cad/src/utilities/debug.py
index 4f402f880..fbd99b0b9 100755
--- a/cad/src/debug.py
+++ b/cad/src/utilities/debug.py
@@ -32,7 +32,7 @@ Bruce 071107 split out two modules by Will:
 """
 
 import sys, os, time, traceback
-from constants import noop
+from utilities.constants import noop
 import foundation.env as env
 from utilities import debug_flags
 
@@ -167,7 +167,7 @@ def legally_execfile_in_globals(filename, globals, error_exception = True):
     execute the python commands in the given file, in this process.
     """
     try:
-        import gpl_only
+        import platform.gpl_only as gpl_only
     except ImportError:
         msg = "execfile(%r): not allowed in this non-GPL version" % (filename,)
         print msg #e should be in a dialog too, maybe depending on an optional arg
@@ -186,7 +186,7 @@ def legally_exec_command_in_globals( command, globals, error_exception = True ):
     in this process.
     """
     try:
-        import gpl_only
+        import platform.gpl_only as gpl_only
     except ImportError:
         msg = "exec is not allowed in this non-GPL version"
         print msg #e should be in a dialog too, maybe depending on an optional arg
@@ -204,7 +204,7 @@ def exec_allowed():
     are exec and/or execfile allowed in this version of NE1?
     """
     try:
-        import gpl_only
+        import platform.gpl_only as gpl_only
     except ImportError:
         return False
     return True
diff --git a/cad/src/debug_prefs.py b/cad/src/utilities/debug_prefs.py
index 065820c07..6fb75fed1 100755
--- a/cad/src/debug_prefs.py
+++ b/cad/src/utilities/debug_prefs.py
@@ -14,8 +14,8 @@ History:
 By Bruce, 050614
 """
 
-from constants import noop
-from constants import black, white, red, green, blue, gray, orange, yellow, magenta, pink
+from utilities.constants import noop
+from utilities.constants import black, white, red, green, blue, gray, orange, yellow, magenta, pink
 
 from utilities.Comparison import same_vals
 
@@ -136,7 +136,7 @@ class Pref:
         ## don't do this: self._fulfill_call_with_new_value()
         return
     def _fulfill_call_with_new_value(self):
-        from debug import print_compact_traceback # do locally to avoid recursive import problem
+        from utilities.debug import print_compact_traceback # do locally to avoid recursive import problem
         func = self.__call_with_new_value_function
         if func is not None:
             val = self.current_value()
@@ -175,7 +175,7 @@ class Pref:
         how to do this depends on datatype (#e and someday on other prefs!)
         """
         def newval_receiver_func(newval):
-            from debug import print_compact_traceback # do locally to avoid recursive import problem
+            from utilities.debug import print_compact_traceback # do locally to avoid recursive import problem
             assert self.dtype.legal_value(newval), "illegal value for %r: %r" % (self, newval)
                 ###e change to ask dtype, since most of them won't have a list of values!!! this method is specific to Choice.
             if self.current_value() == newval: #bruce 060126; revised 060209 to use self.current_value() rather than self.value
@@ -196,7 +196,7 @@ class Pref:
                 env.history.message(msg, quote_html = True, color = 'gray') #bruce 060126 new feature
             for sub in self.subscribers[:]:
                 #bruce 060213 new feature; as of 070613 this also supports the call_with_new_value feature
-                from debug import print_compact_traceback # do locally to avoid recursive import problem
+                from utilities.debug import print_compact_traceback # do locally to avoid recursive import problem
                 try:
                     unsub = sub()
                 except:
@@ -368,7 +368,7 @@ def submenu_from_name_value_pairs( nameval_pairs,
                                    defaultValue = None
                                    ):
     #bruce 080312 revised to use same_vals (2 places)
-    from debug import print_compact_traceback # do locally to avoid recursive import problem
+    from utilities.debug import print_compact_traceback # do locally to avoid recursive import problem
     submenu = []
     for name, value in nameval_pairs:
         text = name
diff --git a/cad/src/icon_utilities.py b/cad/src/utilities/icon_utilities.py
index 358653f8c..829536718 100644
--- a/cad/src/icon_utilities.py
+++ b/cad/src/utilities/icon_utilities.py
@@ -26,8 +26,8 @@ as io for now. (Another possibility would be platform.) [bruce 071214]
 import os, sys
 from utilities import debug_flags
 from PyQt4 import QtGui
-import Initialize
-import EndUser
+import utilities.Initialize as Initialize
+import utilities.EndUser as EndUser
 
 # This is the subdirectory component "ui" at the end of "cad/src/ui",
 # in which we store most icons and similar image files.
diff --git a/cad/src/objectBrowse.py b/cad/src/utilities/objectBrowse.py
index 3f4f575d2..3f4f575d2 100644
--- a/cad/src/objectBrowse.py
+++ b/cad/src/utilities/objectBrowse.py
diff --git a/cad/src/parse_utils.py b/cad/src/utilities/parse_utils.py
index dc0636c03..dc0636c03 100755
--- a/cad/src/parse_utils.py
+++ b/cad/src/utilities/parse_utils.py
diff --git a/cad/src/prefs_constants.py b/cad/src/utilities/prefs_constants.py
index 3bc7fb1ef..c0129c43c 100755
--- a/cad/src/prefs_constants.py
+++ b/cad/src/utilities/prefs_constants.py
@@ -35,9 +35,9 @@ getDefaultWorkingDirectory.
 
 ### do no imports that would not be ok for constants.py to do! ###
 
-from constants import yellow, pink, red, black, magenta, mustard
-from constants import blue, gray, white, green, lightgray
-from constants import ave_colors, diTUBES
+from utilities.constants import yellow, pink, red, black, magenta, mustard
+from utilities.constants import blue, gray, white, green, lightgray
+from utilities.constants import ave_colors, diTUBES
 
 import sys, os # for getDefaultWorkingDirectory
 
diff --git a/cad/src/qt4transition.py b/cad/src/utilities/qt4transition.py
index e20fce42f..55892a602 100755
--- a/cad/src/qt4transition.py
+++ b/cad/src/utilities/qt4transition.py
@@ -11,10 +11,10 @@ import sys
 import traceback
 import types
 
-import debug_prefs
-import debug
+import utilities.debug_prefs as debug_prefs
+import utilities.debug as debug
 
-from objectBrowse import objectBrowse
+from utilities.objectBrowse import objectBrowse
 
 __already = { }
 
diff --git a/cad/src/version.py b/cad/src/utilities/version.py
index 811957a3c..36f0ea199 100755
--- a/cad/src/version.py
+++ b/cad/src/utilities/version.py
@@ -50,7 +50,7 @@ Will Ware"""
 class Version:
     """
     Example usage:
-    from version import Version
+    from utilities.version import Version
     v = Version()
     print v, v.product, v.authors
     """
diff --git a/cad/src/DebugMenuMixin.py b/cad/src/widgets/DebugMenuMixin.py
index 795705a75..f6e5371de 100644
--- a/cad/src/DebugMenuMixin.py
+++ b/cad/src/widgets/DebugMenuMixin.py
@@ -33,17 +33,17 @@ from PyQt4.Qt import QFontDialog, QInputDialog
 
 import foundation.env as env
 from utilities import debug_flags
-import debug
-import debug_prefs
+import utilities.debug as debug
+import utilities.debug_prefs as debug_prefs
 
 from ne1_ui.UserPrefs import save_window_pos_size, load_window_pos_size
-from prefs_constants import mainwindow_geometry_prefs_key_prefix
-from debug import registered_commands_menuspec
-from debug import print_compact_traceback
-from debug import debug_timing_test_pycode_from_a_dialog
-from debug import debug_run_command
-from constants import debugModifiers
-from constants import noop
+from utilities.prefs_constants import mainwindow_geometry_prefs_key_prefix
+from utilities.debug import registered_commands_menuspec
+from utilities.debug import print_compact_traceback
+from utilities.debug import debug_timing_test_pycode_from_a_dialog
+from utilities.debug import debug_run_command
+from utilities.constants import debugModifiers
+from utilities.constants import noop
 
 
 # enable the undocumented debug menu by default [bruce 040920]
@@ -113,7 +113,7 @@ class DebugMenuMixin:
         version if one is present) or unless it uses it independently from this mixin
         and wants to be self-contained.]
         """
-        from menu_helpers import makemenu_helper
+        from widgets.menu_helpers import makemenu_helper
         return makemenu_helper(self, menu_spec, menu)
     
     def debug_menu_items(self):
@@ -342,7 +342,7 @@ class DebugMenuMixin:
         return
 
     def _debug_force_sponsor_download(self):
-        from Sponsors import _force_download
+        from sponsors.Sponsors import _force_download
         _force_download()
         return
 
diff --git a/cad/src/NE1ToolBar.py b/cad/src/widgets/NE1ToolBar.py
index 6e604dc3e..6e604dc3e 100755
--- a/cad/src/NE1ToolBar.py
+++ b/cad/src/widgets/NE1ToolBar.py
diff --git a/cad/src/NE1_QToolBar.py b/cad/src/widgets/NE1_QToolBar.py
index bd02dded7..e54a1f60d 100644
--- a/cad/src/NE1_QToolBar.py
+++ b/cad/src/widgets/NE1_QToolBar.py
@@ -11,8 +11,8 @@ Command Toolbar).
 
 from PyQt4 import QtGui
 from PyQt4.Qt import Qt, QToolBar, SIGNAL
-from icon_utilities import getpixmap
-from debug import print_compact_stack
+from utilities.icon_utilities import getpixmap
+from utilities.debug import print_compact_stack
 
 DEBUG = False # Do not commit with DEBUG set to True.
 
diff --git a/cad/src/StatusBar.py b/cad/src/widgets/StatusBar.py
index 295b6d40d..3e3995d9a 100755
--- a/cad/src/StatusBar.py
+++ b/cad/src/widgets/StatusBar.py
@@ -32,12 +32,12 @@ Majorly rewritten/refactored by Eric M circa 12/2007 [bruce comment 071228]
 import os, time
 from PyQt4.Qt import QProgressBar, QFrame, QToolButton, QIcon, QLabel, SIGNAL, QMessageBox, QStatusBar
 from utilities import debug_flags
-from PlatformDependent import hhmmss_str #bruce 060106 moved that function there
+from platform.PlatformDependent import hhmmss_str #bruce 060106 moved that function there
 import foundation.env as env
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 from utilities.Log import redmsg #bruce 060208 fix bug in traceback printing re bug 1263 (doesn't fix 1263 itself)
-from qt4transition import qt4todo
-from debug import print_compact_traceback
+from utilities.qt4transition import qt4todo
+from utilities.debug import print_compact_traceback
 
 class StatusBar(QStatusBar):
     def __init__(self, win):
diff --git a/cad/src/menu_helpers.py b/cad/src/widgets/menu_helpers.py
index bfde86ee7..580fe75f7 100644
--- a/cad/src/menu_helpers.py
+++ b/cad/src/widgets/menu_helpers.py
@@ -72,7 +72,7 @@ def makemenu_helper(widget, menu_spec, menu = None):
     to which we'll add items; otherwise we create our own QMenu
     and add items to it.
     """
-    from debug import print_compact_traceback
+    from utilities.debug import print_compact_traceback
     import types
     if menu is None:
         menu = QMenu(widget)
@@ -182,7 +182,7 @@ def insert_command_into_menu(menu, menutext, command, options = (), position = -
                 iconset = option[1]
                 if type(iconset) is types.StringType:
                     filename = iconset
-                    from icon_utilities import imagename_to_pixmap
+                    from utilities.icon_utilities import imagename_to_pixmap
                     iconset = imagename_to_pixmap(filename)
                 if isinstance(iconset, QPixmap):
                     # (this is true for imagename_to_pixmap retval)
diff --git a/cad/src/prefs_widgets.py b/cad/src/widgets/prefs_widgets.py
index 52d0d2ff1..ea0eb23f1 100755
--- a/cad/src/prefs_widgets.py
+++ b/cad/src/widgets/prefs_widgets.py
@@ -24,7 +24,7 @@ calling this a "ui/widgets" module without splitting it -- we'll see.
 """
 
 import foundation.env as env # for env.prefs
-from debug import print_compact_traceback
+from utilities.debug import print_compact_traceback
 
 from foundation.changes import Formula
 from widgets.widget_helpers import RGBf_to_QColor
diff --git a/cad/src/widgets/simple_dialogs.py b/cad/src/widgets/simple_dialogs.py
index a894a5d32..8ddc26f5d 100644
--- a/cad/src/widgets/simple_dialogs.py
+++ b/cad/src/widgets/simple_dialogs.py
@@ -10,7 +10,7 @@ TODO: merge some of them into one function.
 """
 
 from PyQt4.Qt import QInputDialog, QLineEdit, QDialog
-from icon_utilities import geticon
+from utilities.icon_utilities import geticon
 
 def grab_text_using_dialog( default = "", 
                             title = "title", 
diff --git a/cad/src/widget_controllers.py b/cad/src/widgets/widget_controllers.py
index f85125158..41bc12ae8 100755
--- a/cad/src/widget_controllers.py
+++ b/cad/src/widgets/widget_controllers.py
@@ -16,7 +16,7 @@ widget_controllers.py - miscellaneous widget-controller classes
 # (can that just be the program env as a whole?)
 
 from PyQt4.Qt import QIcon, SIGNAL
-from qt4transition import qt4todo
+from utilities.qt4transition import qt4todo
 
 import foundation.env as env
 
@@ -28,7 +28,7 @@ def _env_imagename_to_QIcon(imagename, _cache = {}): ### to be replaced with env
         pass
     
     ## pixmap_fname = imagename # stub
-    from icon_utilities import imagename_to_pixmap
+    from utilities.icon_utilities import imagename_to_pixmap
     pixmap = imagename_to_pixmap(imagename)
     pixmap_fname = pixmap # will this arg work too?
     
@@ -167,7 +167,7 @@ class realtime_update_controller: #bruce 060705, consolidate code from runSim.py
         self.checkbox = checkbox
         self.checkbox_prefs_key = checkbox_prefs_key
         if checkbox and checkbox_prefs_key:
-            from prefs_widgets import connect_checkbox_with_boolean_pref
+            from widgets.prefs_widgets import connect_checkbox_with_boolean_pref
             connect_checkbox_with_boolean_pref(checkbox , checkbox_prefs_key)
     def set_widgets_from_update_data(self, update_data):
         if update_data:
diff --git a/cad/src/widgets/widget_helpers.py b/cad/src/widgets/widget_helpers.py
index 9ad7fbc9b..8e5bfb593 100755
--- a/cad/src/widgets/widget_helpers.py
+++ b/cad/src/widgets/widget_helpers.py
@@ -31,7 +31,7 @@ from PyQt4.Qt import QSize
 from PyQt4.Qt import QMessageBox
 
 
-from qt4transition import qt4todo
+from utilities.qt4transition import qt4todo
 
 # ==
author	Eric Messick <ericm@nanorex.com>	2008-03-14 04:44:50 +0000
committer	Eric Messick <ericm@nanorex.com>	2008-03-14 04:44:50 +0000
commit	bcacffeade3f8571f4ba9f7545e0e1afeab8b072 (patch)
tree	6c93c2690a3649102452967e1b3939704a2404fb
parent	1ff69ade95165adbeb0eae702be3731a7b5e70bb (diff)
download	nanoengineer-theirix-bcacffeade3f8571f4ba9f7545e0e1afeab8b072.tar.gz nanoengineer-theirix-bcacffeade3f8571f4ba9f7545e0e1afeab8b072.zip