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

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?

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.

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.

I finally sorted out that the issue was due to an issue with one of the submodules. Simply renaming the repo directory caused a conflict with that submodule. After seeing the discussion in https://stackoverflow.com/questions/9878860/how-can-i-rename-a-git-repository-with-submodules I realized that cloning the repo is a better way to go instead of renaming the directory and that solved the issue with the submodule.

In my case the problem was the .git/HEAD file didn't point anywhere, it just contained a sequence of strange characters. I copied the contents of .git/ORIG_HEAD to .git/HEAD and it worked again.

Source

I solved this issue by reseting all git-submodules with

rm -rf .git/modules
git submodule update --init

Following @ax003d answer, you could replace all old paths (old/path) with the new path (new/path) using this command:

find . -type f \( -name ".git" -o \( -path "*.git/modules/*" -name config \) \)  -print0 | xargs -0 sed -i -e "s#old/path#new/path#g"

You might want to check what the old paths look like before replacing them:

find . -type f \( -name ".git" -o \( -path "*.git/modules/*" -name config \) \)  -print0 | xargs -0 grep --colour "old/path"

Solution :

1. Look into the HEAD file (under .git) -> If it is corrupted (contains some random values), replace the content with this text 'ref: refs/heads/develop' (develop is the last branch I was working on)

2. try - git status.

3. If step 2 doesn't solve your issue, try these commands (may not work for all but worth a try)

rm -f .git/index git reset

4. git will give you unstaged files after reset. keep or discard as per your wish

I was facing this issue with submodules as well, but after analyzing the two files

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

I realized that in my case this was not an issue.

After a little research I have found that in my case I had to add the git (command : module add git) and the error disappeared.