GitHub does not let me access Subfolders

Question

Short:

GitHub has grayed out folders in my repo that I cannot access. This worries me, as my code changes are in those folders!

Long:

I am developing a ZF2 web application and using git for source control. ZF2 is modular, so somewhere somehow (most likely with composer.phar or possibly with git clone) I have downloaded some ZF2 modules into project subfolders. One such ZF2 module is vendor/coolcsn/csn-user. I have made changes in that ZF2 module.

Problem 1: when I run git status, I get this:

$ git status
# On branch master
# Changes not staged for commit:
#       modified:   vendor/coolcsn/csn-user (modified content, untracked content)

When I run git commit, it says "No changes added to commit". And I've definitely made some changes.

So then I found that I can change my directory to vendor/coolcsn/csn-user, and do git status and git commit there. Then I can change back to the root directory of the project, and do a git commit there. Then, all is fine.... until:

Problem 2: Until I do a git push to GitHub. On GitHub my entire project seems to be in place, but the vendor/coolcsn/csn-user is not accessible on GitHub! It is Grayed Out. I cannot click on it. It makes me cry. I don't know why and I don't know what's up. I've read something about git submodules. I don't know if I have git submodules or if they are something else. I have not consciously set up any submodules myself. Either way, I am concerned that my GitHub submodule changes are not being tracked, or if they are being tracked, they are hidden, not accessible for viewing.

Possible Solution #1: I thought that I could REMOVE .git folder in the submodules (if they are submodules) and just do straight commits to GitHub, with my csn-user folder possibly not being grayed out. But before I do so, I've heard that it is not advisable, and I wanted to check on what all that is going on, and how if anyhow, I can properly use git and GitHub and submodules, and track my changes at the same time.

In particular, looking for a set of steps, instructions, or ideas on how keep my repo accessible and committable both using git and GitHub.

Answer 1

If you do have submodule, and running git submodule status to check that out, make sure to:

• not run the command from a subfolder of your local Git repository
• or use Git 2.25 (Q1 2020)

That is because, before Git 2.25 (Q1 2020), "git submodule status" that is run from a subdirectory of the superproject did not work well. That has been corrected.

See commit 1f3aea2 (25 Nov 2019) by Manish Goregaokar (Manishearth).
^{(Merged by Junio C Hamano -- gitster -- in commit 88cf809, 05 Dec 2019)}

submodule: fix 'submodule status' when called from a subdirectory

^{Signed-off-by: Manish Goregaokar}

When calling [git submodule](https://git-scm.com/docs/git-submodule) status while in a subdirectory, we are incorrectly not detecting modified submodules and thus reporting that all of the submodules are unchanged.

This is because the submodule helper is calling diff-index with the submodule path assuming the path is relative to the current prefix directory, however the submodule path used is actually relative to the root.

Always pass NULL as the prefix when running diff-files on the submodule, to make sure the submodule's path is interpreted as relative to the superproject's repository root.

Answer 2

I have the same issue and got resolved by doing the following.

I was trying to synch my local repo to my github repo, but could not due to subfolders having been git initialized by mistake. Once the entries were removed and re-initialed the local state is reflected on my github repo.

1. removed all the .git folders from the sub folders as well as from root.
2. git init
3. git add .
4. git commit -m "first commit"
5. git branch -M master (if you are committing from the branch switch to branch)
6. git remote remove origin (if you have any)
7. git remote add origin https://github.com/abcd1234/xxxxxxx.git
8. git push -u origin master