conditions are other images, plus the _nonISO is added

Implemented as additional call to ChrRenderIntoTerritoryFiles()
from ChrRenderIntoTerritories(), the call is however guarded by
config file directive "produce chromatin density images"

     added Cell::GetCurrentPhaseID(),
     added ReportCellPhaseID() and check for "CellCyclePhase:" in logs.

Sample call: ../mitogen  -c ../../config/config-smallVOI-highSNR.ini -g ../test2/initial_mask_after_005.ics |tee log.txt

     Displays it as non-bleached rendering of the chromatin, density basically.
     If thresholded >= 1, one gets occurence mask.

M    src/toolbox/collisions.cpp

M    src/cellScm.cpp

be Mitocheck-specifically re-adjusted because this value is considered when creating local masks
for the atomic phase functions (and Mitocheck does BIG translations and the cellLookDistance found
in our configs is typically not large enough to allow to create large enough local masks).
M    src/cell.h

the rendered cell plus 2px wide border (as the least safe extension). Thus, the target
mask image, into which the cell is finally rendered/copied, must have borders large
enough to host this small extra border -- which is usually the case as local mask of phase
functions are created with generous borders...
M    toolbox/bp_lists.cpp

ScmNewCellPositionCollide() functions do not let cell approach border closer than 2px.
This becomes essential when rendering the cell into the sceneMasks, as explained above.
M    cellScm.cpp

M    CMakeLists.txt
M    src/cellChr.cpp
M    src/scheduler.cpp

Added the new functionality into the main rnd walk file.
Added a new Get/Set function to the rnd walk class.
M    src/toolbox/randWalk.h

Uses now the 3D walk for "universal cell movement".
M    src/cellScm.cpp

3D-related initialization of the rnd wlk in the cell's constructor.
M    src/cell.h

Added/updated the reports.
M    src/main.cpp

Introduced a new parameter: the anisotropy along the z-axis of the 3D random walk.
M    config/config-middleVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config-synthHeLa/small_masks/config-synthHela.ini
M    config-synthHeLa/standard_masks/config-synthHela.ini

M    bp_lists.cpp

which lead to some rendering issue ("pixelShift has negative values" error).

Typos in the docs were corrected.
M    src/toolbox/collisions.h

Thresholding of the correlation results into a freePositions image prevents
flagging the border pixels as free (=available to occupy).
Removed some ages-long deprecated code.
M    src/toolbox/collisions.cpp

Only added comments/documentation to the parameters of Cell::GenerateNucleolus().
M    src/cell.cpp

Very decent reformating of a small portion of the code.
Corrected bug that prevented second nuclei (after split) to be rendered
when macro ENABLE_NUCLEOLI was disabled.
M    src/cell_04_Telophase.cpp

HeLa sequence used in the TMI paper. There are two versions available:

small_masks: the simulation happens directly at the original resolution of the real HeLa videos
standard_masks: the simulation happens at about twice better spatial resolution

Temporal resolution used in the configurations files is comparable to the one of the real videos.

A    config-synthHeLa
A    config-synthHeLa/small_masks
AM   config-synthHeLa/small_masks/initialI.ics
A    config-synthHeLa/small_masks/config-synthHela.ini
AM   config-synthHeLa/small_masks/initialII.ics
A    config-synthHeLa/start2.sh
A    config-synthHeLa/init_positions_in_microns.txt
A    config-synthHeLa/init_positions_in_microns2.txt
A    config-synthHeLa/standard_masks
AM   config-synthHeLa/standard_masks/initialI.ics
A    config-synthHeLa/standard_masks/config-synthHela.ini
AM   config-synthHeLa/standard_masks/initialII.ics

calculation of MSD curves.

New flag "report for 2D MSD analysis = 1" was introduced into the testing section.
M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini


Cell::ScmRenderCellIntoMask() has new parameter: a time value to possibly report.
M    src/cell.h
M    src/cellScm.cpp

Adjusted lines whereever the above function is used.
M    src/cell.cpp
M    src/cell_00_Samplephase.cpp
M    src/cell_01_Prophase.cpp
M    src/cell_02_Metaphase.cpp
M    src/cell_03_Anaphase.cpp
M    src/cell_04_Telophase.cpp
M    src/cell_05_Cytokinesis.cpp
M    src/cell_06_G1Phase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_08_G2Phase.cpp

- added some missing parts of the RndWlk (the part around mean step size distribution)
- configuration that enables Mitocheck-like behaviour moved from 'testing' section into the 'cell' one
- following the Mitocheck-like behaviour during simulation is no longer communicated as a "TESTING MODE"

M    config/config-middleVOI-lowSNR.ini
M    config/config-smallVOI-highSNR.ini
M    config/config-711extVOI-highSNR.ini
M    config/config-smallVOI-lowSNR.ini
M    config/config-middleVOI-highSNR.ini
M    src/cell.cpp
M    src/cellScm.cpp
M    src/cell.h

Added some more debug to figure out why we are getting some rendering error.
(error msg: pixelShift has negative coordinates)
M    src/toolbox/bp_lists.cpp

M    CMakeLists.txt
M    Doxyfile
M    src/cell.cpp
M    src/cell.h
M    src/cell_00_Samplephase.cpp
M    src/cell_01_Prophase.cpp
M    src/cell_02_Metaphase.cpp
M    src/cell_03_Anaphase.cpp
M    src/cell_04_Telophase.cpp
M    src/cell_05_Cytokinesis.cpp
M    src/cell_06_G1Phase.cpp
M    src/cell_07_SPhase.cpp
M    src/cell_08_G2Phase.cpp
M    src/dots.h
M    src/main.cpp
M    src/molecule.h
M    src/scheduler.h
M    src/settings.h
M    src/toolbox/bp_lists.h
M    src/toolbox/cell_movement.h
M    src/toolbox/collisions.h
M    src/toolbox/deformations.h
M    src/toolbox/finalpreview.h
M    src/toolbox/flowfields.h
M    src/toolbox/importexport.h
M    src/toolbox/perlin.h
M    src/toolbox/randWalk.h
M    src/toolbox/rnd_generators.h
M    src/toolbox/shape_rendering.h
M    src/toolbox/user_abort.h
M    src/types.h

M    Doxyfile

M    Doxyfile

M    src/main.cpp

chromatin repairs are effective/on.

M    src/main.cpp

for creating local single-cell masks has been "enhanced". That is,
the new created local image considers only 80% of the simulation
(it still does not consider sceneMasks, though).

M    src/toolbox/bp_lists.cpp
M    src/toolbox/bp_lists.h