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?

Hissing

Are you nesting git repositories? – Bendix

@Bendix I do have several submodules, however this issue is with the main repo. – Hissing

Answer 1

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 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.

Hissing

Recovering from this problem only takes two small manual edits per submodule. For me that's easier than re-cloning the repository and all its submodule(s). – However

@JoshFarneman How should I (newbie) understand what you've done. pls provide clear code before and after. so one can understand what is required. – Soni

But what If I don't want to lose my local branches. ? Please help me what to do in such a scenario. – Beore

Answer 2

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.

Cachepot

Thank you, this worked well for me. However, the second path was a bit shorter for me: .git/modules/{submodule}/config (I'm using git version 1.7.9.5 on Ubuntu) – However

I just moved from PC to Mac and having the same problem. I updated the path in those two files, and the new path is correct, but I'm still getting fatal: Not a git repository. There is a .git file in that location, so maybe I'm missing something else? – Pamphleteer

Just a note here, for me the config file has a relative path unlike the .git file. – Balthazar

Answer 3

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.

Muley

I know this is an old answer but just to let other people know: it's still a good answer in 2018. Thank you! – Hecate

Answer 4

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

Retrospect

Answer 5

I solved this issue by reseting all git-submodules with

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

Leigha

Wow! Just worked for me! In my case I accidentally made a "rm -r" with no wildcard matching. It wiped a couple of files from the project root before being stopped for some prompt. – Bartholemy

Answer 6

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"

Crock

Answer 7

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

Caducous

Thank you, this fixed it for me. I'm guessing my HEAD file somehow got corrupted. No submodules like OP, just simply receiving the dreadful "Fatal: not a git repository" all of a sudden out of nowhere – Romanaromanas

This happened to me when i was doing git checkout then it hanged so i restarted the pc. thank you mate. – Goodbye

Answer 8

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.

Ingrown

In Linux command prompt while running - module add got, I get the following error. module: command not found – Char