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The git addin keeps file locks, even after closing the solution. This causes commandline git gc to fail:
$ git gc
Counting objects: 238661, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (44816/44816), done.
Writing objects: 100% (238661/238661), done.
Total 238661 (delta 193170), reused 237867 (delta 192516)
rm: cannot unlink `pack-20b7c0158f91a487dfc3c545473fa021e470babc.pack': Permission denied
rm: cannot unlink `pack-c2e5bd5fb22db1a49824fac9b3aeeb867fd08603.pack': Permission denied
I believe JGit has fixed this issue as I cannot repro with the latest version of NGit. I can even gc from the commandline while monodevelop has a solution open.