Git status reports deleted files which still exist

Question

My Git status is showing all files deleted in my working tree which is incorrect, they are still there.

To resolve it, I should execute git reset --hard which reset all my modifications to other files.

Any idea how to solve it or how did it happen?

git status output:

On branch develop
Your branch is behind 'origin/develop' by 15 commits, and can be fast-forwarded.

Changes to be committed:
(use "git reset HEAD <file>..." to unstage)

deleted:    .gitignore
deleted:    v3/.gitignore
deleted:    v3/index-test.php
deleted:    v3/index.php
deleted:    v3/protected/.gitignore
deleted:    v3/protected/.htaccess
deleted:    v3/protected/Gruntfile.js

Edit: The above is not the complete git status output. Those files that I was working on are not staged for deletion.

Freehearted

It's helpful to show the output here, even if it's trimmed a bit and paths are obscured. Also, it's helpful to talk about what you did leading up to this issue. It sounds to me like the files are staged for delete in the index, but present in the working copy. But I can't really tell from your description. – Merthiolate

yes, they are staged for delete. I'll add the git status output to the question. – Freehearted

Is that the entirety of your git status output, or did you snip it? The reason I ask is because you say you have modifications to other files, and from your git status output, it doesn't appear that way. – Merthiolate

That's not the entire status output, those files that I was working on are not staged – Freehearted

Answer 1

If the only issue is that the some files have been removed from the index, but are still in the working tree, then all you need to do is:

git reset

By default, git reset defaults to mixed mode which does this:

--mixed

Resets the index but not the working tree (i.e., the changed files are preserved but not marked for commit) and reports what has not been updated. This is the default action.

So it will leave your changes intact but unstage everything. If you find that the files are actually missing, then you'll need to check them out to restore them:

git checkout -- path/to/file/or/dir

You could parse the short form of git status using cut and xargs to help do this if you have lots of files. I'll leave that as an exercise for the reader though, since you're claiming that all the files are there.

Merthiolate

git resetworked for me after cloud sync seemingly messed up the folder. Thanks! – Physiognomy

Answer 2

if you deleted a file from local disk using

rm file.name

and if file.name was already checked into git. Then you should actually issue this command

git rm file.name

to tell git that you don't want it to track that file anymore

Ralaigh

Answer 3

  git co my_annoying_file
  git rm my_annoying_file
  git commit -m "removing annoying file"

now they are truly deleted from git tracking

...also git reset --hard may be to brittle for this scenario, consider git reset HEAD my_annoying_file

Emalia

thanks. but it's not just a single annoying file.. it's the whole working tree. – Freehearted

same should apply to folder, but it sounds like you have git repository inside git repository. Try to check if you have folder called .git in that folder that causing an issue – Emalia

there is a .git directory which belongs to git-flow, will double check if that's the source of problem. thanks. – Freehearted

Answer 4

I had a similar issue where I have my git repo in a folder synced by OneDrive. I'm guessing it was caused by some syncing process. I tried to no avail:

• Stashing the changes
• Committing the changes and then git reset --hard HEAD^
• Myriad other variations of git reset...

---

Then I tried:

• Reverting the restoring the "deleted" files via git but it couldn't because the gitlog said "files already exist".
• Next, in the file explorer I cut all my files in the repo and pasted them somewhere else on my machine outside of the repo, then I let git restore the files and it was happy.

This was manageable for me as this repo is my Dendron repo so it was about 450 simple text files. So, this approach may not be feasible for all.

Bekah

Don't sync your Git repository with OneDrive. It can corrupt the repository at the blink of an eye. Revived worktree files are the least of the problems that you can run into. You have been warned. – Kinematics