Two last corrections:
- Viewport was not written during automatic export of XML files, because Virtualization of XMLSettingsTree did not work due to inconsistent function definition (const vs. non-const)
- Some of the default parameter-file had "Start saving movie frames" switched on by default, dramatically slowing down the example runs. Now it is switched off in all example XML files.

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/tutorial5_init.xml
changed src/VirtualLeaf.cpp
changed src/mainbase.cpp
changed src/mainbase.h

Uncompressed XML files.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed data/leaves/tutorial1_init.xml
changed data/leaves/tutorial2_init.xml
changed data/leaves/tutorial3_init.xml
changed data/leaves/tutorial4_init.xml
changed data/leaves/tutorial5_init.xml

Some last fine-tuning
- File dialogs start from appropriate data directories
- XML files contain right values for datadir
- Reordered parameter dialog
- Added new "make perl" heading to the makefile
- Corrected segfault for batch mode

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed data/leaves/tutorial1_init.xml
changed data/leaves/tutorial2_init.xml
changed data/leaves/tutorial3_init.xml
changed data/leaves/tutorial4_init.xml
changed data/leaves/tutorial5_init.xml
changed src/Makefile
changed src/VirtualLeaf.cpp
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h

In response to referee's comment:

"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in

rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked

automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."

I made the following changes:

- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.


--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h

Increased auxin_growth LeafML file's storage_slide from 10 to 100.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml

Use iteration number instead of time stamp to tag exported cell data files. Added default LeafML files to tutorials 3-5. See respective ChangeLogs for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
changed src/ChangeLog
changed src/TutorialCode/Tutorial3/ChangeLog
changed src/TutorialCode/Tutorial3/tutorial3.h
changed src/TutorialCode/Tutorial4/ChangeLog
changed src/TutorialCode/Tutorial4/tutorial4.h
changed src/TutorialCode/Tutorial5/ChangeLog
changed src/TutorialCode/Tutorial5/tutorial5.h
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h

Export Cell Data at interval specified in the leafML file or explicitly via the file menu.
Added new parameters to VirtualLeafpar.tmpl
Added GPL boilerplate to make_{parameter,pardialog}_source.pl files.
Added new parameters to auxin_growth.xml. See respective ChangeLog files for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed src/ChangeLog
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/perl/ChangeLog
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl