Git: fatal: Pathspec is in submodule

I'm trying to get TravisCI to automatically deploy my Hakyll static site, according to this guide.

Here's how my repo is set up. I have my source branch, which contains my hakyll and markdown files. It builds the html into the _site directory, which is set up as a submodule, linked to my master branch.

I build the site without problem, then cd into the _site directory. However, when I try to git add ./* the newly generated HTML files, I get the following error:

fatal: Pathspec './about.html' is in submodule '_site'

When I try git add --all, I get this error:

git: pathspec.c:317: prefix_pathspec: Assertion `item->nowildcard_len <= item->len && item->prefix <= item->len' failed.

/home/travis/build.sh: line 245: 1566 Aborted git add --all

What is causing this, and how can I avoid this?

You can view the repository here.

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.