I take it those files are needed in the repo because the tools need them to be there, at least for starting the first time. But the tools change them as you work.
If so, you can move them to a subdir in the repo, then add a script that copies them. The script should be started (only) the first time thus it can be added as a target in the new Makefile.
If needed, add crc check to see if the repo'ed version changed (look at it as if it was the template). Upon a failed check, the template in the subdir and the actual user modified copy should be merged. I dont know if its needed.