If you are not using it, just get rid of it. I would never ship any file relating to version control in the dist so would not add it to the MANIFEST. The only files needed in the dist are those which a user requires in order to build, test and install the dist.

That said, it will be worth your while to look into using version control sooner or later. You've started using git for other tasks so maybe you could think about putting this code into a git repo also?