git status returns fatal: Not a git repository but .git exists and HEAD has proper permissions

Question

When I run git status on my repo I get fatal: Not a git repository: /my repo/.git/modules/docs

I've checked and .git exists and contains HEAD with the proper permissions. I can run various other commands fine. If I run git gui it opens fine and will list a couple of the changed files, but is missing a lot of them.

I'm guessing there may be some sort of corruption in HEAD, not sure though. Any idea how to fix this without wiping out the whole repo?

Update: I realized that I had changed the name of the repo's directory. The directory being referenced in the error is the old name of the directory. So my current repo is at /new dir/.git but the error is saying Not a git repository: /old dir/.git/modules/docs. So maybe git is confused?

Answer 1

These two files contains absolute submodule path:

{submodule}/.git .git/modules/{submodule}/config 

So, if you moved the repo, the absolute path in these two files are not valid, and cause the 'not a git repository' error. Just fix these files manually.

Answer 2

Former versions of git used an absolute path to locate the gitdir of a submodule. The solution is as follows:

1. Upgrade git to the latest version. Some says you'll need at least version 1.7.10. I just successfully solved the issue with git 1.8.3.
2. Delete all the broken submodule folders: rm -rf broken_submodule_folder
3. Update the registered submodules: git submodule update. You should see the submodules being checked out.