Git: fatal: Pathspec is in submodule

Question

Removing the directory from git and adding it again worked for me:

 git rm --cached directory
 git add directory

This works if you purposefully removed the .git directory because you wanted to add directory to your main git project. In my specific case, I had git cloned an extension and ran git add . without thinking too much. Git decided to create a submodule, which I didn't like. So I removed directory/.git and ran into Git: fatal: Pathspec is in submodule. I couldn't find out how to remove the submodule stuff. Fixed with the two lines above.

It seems the git add context is the parent repo ("parent" means the one including the submodule), which triggers the warning.

Try and change its context with:

cd _site
git --git-dir=.git --work-tree=. add . 
git --git-dir=.git --work-tree=. commit -m "new files"

Don't forget that, if this works, you would still have to go back to the parent repo, and git add _site, since the subrepo would have changes.

And you would have to push both.

---

Update January 2017 (2+ years later)

With Git 2.12, you won't see that prefix_pathspec: Assertion anymore.

See commit 2d81c48 (09 Jan 2017) by Stefan Beller (stefanbeller).
Helped-by: Jeff King (peff), and Junio C Hamano (gitster).
^{(Merged by Junio C Hamano -- gitster -- in commit 00880a1, 18 Jan 2017)}

pathspec: give better message for submodule related pathspec error

Running "git add a/b" when "a" is a submodule correctly errored out, but without a meaningful error message.

It seems my problem is that I was accidentally deleting the .git folder of the submodule.

It sounds like you're operating on non-initialized submodules (they're basically missing .git directories), therefore you should initialize them first and update:

git submodule init
git submodule update

Otherwise if you don't need this submodule anymore, remove it by:

git submodule deinit _site

or:

git rm -f --cached _site

and add it again:

git add _site

Check your current outstanding submodules by: git submodule status.

See also: Why is git erroring with 'Assertion failed' on git add .?

I wanted to make a subdirectory stop being a git submodule. This worked for me:

$ mv subdir subdir2
$ git rm --cached subdir
$ mv subdir2 subdir

100% fix for this problem, even if you have more than one submodule directory inside the project:

> git submodule foreach --recursive deinit -f --all -- <relative path>
> git add --all -f