tying files to git repository

Hi,

I am a developer of scientific software, as science software we expect and encourage users to modify source code in order to customize their experiments. The mechanism which has been developed to do this predates having source code in git and we are trying to figure out a way to minimize changes to the scientists workflow, while leveraging the power of git to improve the process. In the workflow the scientist creates a 'case' using script in the repository to create a directory structure from which they will conduct their experiment. Part of that directory structure is a SourceMods directory where the user can drop modified source files that will be compiled in place of a file of the same name in the source tree. These files are sometimes long lived and passed from case to case and even user to user and it is not hard to have the files get out of sync with the source tree. We have discussed at length removing the SourceMods capability and requiring scientists to create branches in git, but there is a lot of resistance to this in the community. What I would like to explore is allowing scientists to keep the method that they are used to but at the same time tying these modified files to their history in git. Is there a way to get the git metadata associated with an individual file so that we can treat that file as if it were in the repo?