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What would you like to do?
Fixing git submodule AKA git repo inside another git repo

Problem, and symptoms:

You experience one or more of these symptoms

  • you have code in a directory but it's not being pushed to GitHub. You just see an empty directory icon
  • you see this message when you add code to your git repository from the command prompt
hint: You've added another git repository inside your current repository.
hint: Clones of the outer repository will not contain the contents of
hint: the embedded repository and will not know how to obtain it.
hint: If you meant to add a submodule, use:
hint:   git submodule add <url> nodule
hint: If you added this path by mistake, you can remove it from the
hint: index with:
hint:   git rm --cached nodule
hint: See "git help submodule" for more information.

What's happening?

You have added a git repository inside another git repository

The outer git repository will ignore the inner git repository.

The inner git repository is known as a submodule.

Let's say you have these files and directories

   |- file1.html
   |- file2.css
   |- resources
       |- info1.json
       |- info2.json

If you create a git repository in the project directory, and there's a git repository in the resources directory, all the files inside the resources directory will be ignored by the git repository in the project directory.

A git repo inside another git repo is called a submodule. In other words, a directory with a git repository in, is inside another directory, also with a git repository in. The submodule doesn't have to be in the immediate subdirectory, it can be one or two or more levels above.

Sometimes this is what you want to do, but if what you want to do is to collect files from more than one directory together in to one repository, you only want one git repository for the entire project. So a submodule is not what you want to happen.

When a git repo is created, it created a hidden directory called .git and that's how the git tool knows it's working with a git repository. All of the info about your past versions of code, the location of the GitHub remote etc.. are stored in files in this .git directory.

If you have a git repo in the project directory, and another one in the resources directory, your file system will actually look like this,

   |- .git
   |- file1.html
   |- file2.css
   |- resources
       |- .git
       |- info1.json
       |- info2.json

If you add and commit files from the project directory, you'll see an entry for the resources directory under files you've added and committed, but the info1.json and info2.json files will not be added.

If you want the project directory to have one git repo with everything in, follow these steps.

In the resources directory (the inner directory with a git repo in): delete the .git folder. You will need to enable hidden files to see this in explorer / finder.

Use a command prompt or git bash (windows) or terminal (mac, linux) and navigate to the project directory. You need to be in the directory above the one with the submodule - so in this example, the project directory (the outer directory, the one that should contain all the files). Then run the command

git rm --cached resources

but replace resources with your own directory name. The --cached part is really important, if you miss it out it will irreversably delete your resources directory!

Now you should be able to use the git add command to add all of the files in the resources directory to the main project's repository, and commit those files.

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didzis1 commented Sep 30, 2022

If this doesn't work for someone, check if you have a hidden .git directory with ls -la command. If there is one, remove it with rm -rf .git and try to add and commit your files after that.

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Thank you this was very helpful

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Thanks! it was very helpful!

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Thank you! Very Helpful! Have a nice day.

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You rock, thanks!! :)
If anyone is getting permission types of errors when removing stuff - you might need to use -f (force).
I had to use both when removing the .git folder and the --cached resource directory.

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Very grateful! This solves the problem for me. Thank you!

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fatal: pathspec 'frontend' did not match any files

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DaliaO15 commented Feb 2, 2023

Thanks!! I finally understood what was going on.

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Thank you! <3

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Thanks a lot :)

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this helped so much, thank you!

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Thank you for your help with the detailed instructions to fix this issue! The suggested fix worked.

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Kasbe14 commented Mar 29, 2023

error: the following file has staged content different from both the
file and the HEAD:
(use -f to force removal)
am having this error , can someone help me

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qupfer commented Mar 31, 2023

I would rename ".git" to "git" instead removing it.
This has the benefit, you can later revert the renaming (back to .git). After that, you can use git pull or git checkout other-branch again to update/modify the included resource. Rename it again to git and commit.

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SLegrez commented Apr 13, 2023

Thanks a lot !

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Thanks a lot

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This helped me too! Thanks!

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Helped me a lot, thank you so much!

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Thank you so much, just what I was looking for!

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wow this worked really well , iam facing this issue from several days

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fatal: pathspec 'foldername' did not match any files
please help

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Smontan commented Sep 10, 2023

No one says in the stack overflow that .git folder is hidden!. It took me 6hrs before I read this Solution.

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