The gitmodules documentation[1] states that the .gitmodules file is at the root. However, it would be nice if this could be supported in any directory similar to how .gitignore works. Right now git-subrepo does not support submodules inside of a subrepo[2] (I suspect subtrees would have the same problem, but I did not verify). I think this is a limitation of git, rather than subrepo itself. Perhaps there are reasons why .gitmodules must be at the root, but I at least wanted to point it out and see if this could be supported. [1]: https://git-scm.com/docs/gitmodules [2]: https://github.com/ingydotnet/git-subrepo/issues/262