fix for Bug 1940: Improve Windows Menu
-The window menus will now look like this:

  Main Window
  ------
  Close Windows Below:
  ------
  Diagram: ...
  Model Analysis
  Plot: ...
  Slider

-"Close Windows . . ." and dividers won't appear if no
 secondary windows
-renamed slot more accurately (which also had a typo in name)
-let form handle Window menu creation
-allow Alt-'W' keyboard shortcut
- fix for issue 1987: tighten checking of elements, so we don't crash if an element is not where we expect it to be
- Bug 1987: catch potential exceptions to prevent JVM crashes
- fix bug in determning label length
- COPASI left .dot files around wherever executed. For now I moved those behind DEFAULT_DEBUG_TRACING (after all we use COPASI_DEBUG to activate some features, and we want them activated independently of the dot files being created)
- ensured the spelling is COPASI_DEBUG_TRACE, as automatically defined when COPASI_DEBUG is enabled, unless specifically deactivated.
- allow the version in CopasiVersion.h to be overridden by a cmake option. For example: -DCOPASI_OVERRIDE_VERSION="4.11.65" that makes it easier to create builds on platforms without forcing to use the gittools. if not given, the behaviour is as before
- actually set the comment back to source
final version of scatter search, this is ready to roll
removed un-needed #includes.
changed the order in which optimisation algorithms appear (now alphabetic)
fixed compile error:
COPASI/copasi/math/CMathDependencyGraph.cpp:156: error: jump to label 'finish'
COPASI/copasi/math/CMathDependencyGraph.cpp:103: error:   from here
COPASI/copasi/math/CMathDependencyGraph.cpp:124: error:   crosses initialization of 'std::ofstream GetUpdateSequence'
*** [copasi/CMakeFiles/libCOPASI.dir/math/CMathDependencyGraph.cpp.o] Error code 1
Shut down events handling part in CHybridMethodODE45.cpp in function isValidProblem. Event handling part will be improved in branch hyb_event.
Merge branch 'master' of git.copasi.org:COPASI
- fix for Bug 1988: extractId would generate an incorrect id for identifiers from identifiers.org
- change the SBML exporter to export identifiers from identifiers.org, as it will be easier for our users to understand
fix for But 1922: MCA Result Flux Control Coefficient Labeling
-added "(parameters)" and "(observables)" to Row and Columns labels
-disabled mpComboRows and ...Columns when 2 or less Items
-rearranged the "Other" field and label
Fixed cmake files to work with CMake 2.8.11.
Fixed lapack wrap files to work with Apple Accelarate Framework.