Git: fatal: Pathspec is in submodule

Question

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.

Diarist

it might be duplicated of #25458806 be aware the could be a problem of permissions on files https://mcmap.net/q/19900/-git-rm-fatal-pathspec-did-not-match-any-files – Hardie

Answer 1

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.

Ecker

This solved an issue I had where I accidentally pulled down a project into an existing project, creating a submodule. I had tried just about every other suggestion out there. Removing the directory and adding again addressed my problem. Thanks. – Altair

I have .git and see it! But when I want to commit some files that located in a folder, it shows an error "blahblah did not match any file(s) known to git" – Souvenir

This fixed the issue. In my case, I cloned the project in another machine. – Mormon

I was having the same problem with a Visual Studio project which I synch with GitHub. The folder where most of my development is taking place wasn't being tracked, and if I tried adding it I was getting the same error. This solution fixed it for me too! – Scauper

THANK. YOU!!! Took me two days to figure out why my CI/CD build was failing... – Roughrider

Answer 2

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

Begum

Good hack :) Works. – Onwards

I tried removing the .git and .gitignore files in the subdirectory, but it turned out I needed to remove the cache too. Worked, thanks! – Candancecandela

I tried without rename and it still worked, thanks. – Intramundane

Answer 3

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.

Toxicogenic

I get error: unknown option git-dir=.git'`. Also, I can't commit my parent repo from within Travis, that will cause an infinite loop of Travis running... – Diarist

@jmite I have fixed the answer: the --git-dir and --work-tree are options of the git command, not the git add command. Try at least the git add part, if the git commit isn't practical. – Toxicogenic

This seems to break something for me, but I was able to find the solution here – Antonantone

Answer 4

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 .?

Hooch

Answer 5

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

Diarist

I have exactly the same problem. Could you share how you solved it? – Livelihood

I solved it by changing my script to not delete the .git folder. So I'd advise that you check your script, see if you actually have a .git folder in the directory. – Diarist

I do but I want to get rid of it as remote repo no longer exists. It's just easier for us to include its source code as it is. – Livelihood

You're best bet then is to look at changing the remote repos. Take a look at the git remote command. – Diarist

Answer 6

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

Elasticity

deinit learned something new. – Intramundane