Expose git add to CLI and remove add_all= True as default from repo.commit() #116
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This commit exposes the git add function to the CLI via "rdm add" which allows specifying files to be staged.
…om internal function calls
…l add_all flag in PI documentation
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This PR seeks to harmonize CADET-RDM further with the Git Interface, by exposing
git addviardm add, giving the possibility to stage single files instead of adding all with the commit. Secondly, the default setting ofadd_all=Truefor the Python interface methodrepo.commit()is changed toFalse, and the arguments removed from internal function calls respectively. Finanlly, the documentation is updated to make the use of these commands clearer and reflect those changes.