Hi, I just discovered that when you have a slash at the end of a nested repository, the files contained in the repository get added instead of the gitlink. I found this when I was adding a submodule and wanted to commit a small change before that. You get the slash by using tab autocompletion. Here is a recipe to reproduce: mkdir test cd test; git init touch a; git add a; git commit -m a mkdir ../test.git; (cd ../test.git; git init --bare) git remote add origin ../test.git git push origin master git submodule add ../test.git submodule git reset git add submodule/ Now instead of just submodule gitlink there is an entry for submodule/a in the index. I just thought I put this out there. Will have a look if I find the time to cook up a proper testcase and investigate. Cheers Heiko