Merge pull request #736 from TeamCOMPAS/JOSS

JOSS

Copy input files (grid, logfile-definitions) to output container + de…

…fect repairs (#603)

* Enhancement and Defect Repairs:
- Added code to copy any grid file and/or logfile-definitions file specified to output container.
- Copying a large grid file could take time, and take up much space, so added new program option '--store-input-files' which is TRUE by default.  If FALSE, neither the grid file (if specified) nor the logfile-definitions file (if specified) will be copied to the output container (if TRUE, both will be copied (if specified)).
- Fixed issue #600: changed pythonSubmit.py to treat fully-qualified grid filenames and fully-qualified logfile-definitions filenames correctly (i.e. don't add CWD if the filename is already fully-qualified).
- Fixed issue #601: changed pythonSubmit.py to put all boolean parameters on the commandline, with True or False value.

* Update Log.h

Removed extraneous include

CompasHPC improvements (#359)

Merge pull request #373 from TeamCOMPAS/USSN

Fixing defect in supernova resolution

Merge pull request #372 from jeffriley/dev

Code cleanup

Merge pull request #371 from jeffriley/dev

Minor - fix missed change to changelog.h

Merge pull request #370 from TeamCOMPAS/RLOF_output_docs

Rlof output docs

Merge pull request #369 from TeamCOMPAS/Cleaning

Correct resolution of supernovae of ultra-stripped stars

Merge pull request #366 from TeamCOMPAS/UpdateRaysCode

Adding version number

Merge pull request #364 from einshoe/dev

Custom caller/callee profiling option