Tukukkk

I had the same problem on the Mac after cloning a repo, it would assume all files have been changed.

After running git config --global core.autocrlf input it was still marking all files as changed. After looking for a fix I came across .gitattributes file in the home directory which had the following.

* text=auto

I commented it out and any other cloned repositories from now on are working fine. Hope this helps anyone out there.

git config core.fileMode false

solved this problem in my case

https://www.kernel.org/pub/software/scm/git/docs/v1.7.10.1/git-config.html

TL;DR;

core.fileMode

If false, the executable bit differences between the index and the working tree are ignored; useful on broken filesystems like FAT. See git-update-index(1).

The default is true, except git-clone(1) or git-init(1) will probe and set core.fileMode false if appropriate when the repository is created.

I assume you are using Windows. That github page you linked has the details backwards. The problem is that CRLF line endings have been committed to the repo already and because you have core.autocrlf set to either true or input, git wants to convert the line-endings to LF so git status shows that every file is changed.

If this is a repo that you only want to access but have no involvement with you can run the following command to merely hide the issue without actually solving it.

git config core.autocrlf false

The following is taken directly from the gitattributes man page and should be preformed from a clean working directory.

echo "* text=auto" >>.gitattributes

rm .git/index     # Remove the index to force git to

git reset         # re-scan the working directory

git status        # Show files that will be normalized

git add -u

git add .gitattributes

git commit -m "Introduce end-of-line normalization"

If any files that should not be normalized show up in git status, unset their text attribute before running git add -u.

manual.pdf      -text

Conversely, text files that git does not detect can have normalization enabled manually.

weirdchars.txt  text

Please run the following commands. That might solve the issue.

# Remove everything from the index.

git rm --cached -r .



# Write both the index and working directory from git's database.

git reset --hard

In Visual Studio, if you are using Git, you can auto generate the .gitignore and .gitattributes files. The auto generated .getattributes file has the following line:

* text=auto

This line is near the top of the file. We just needed to comment the line out by adding a # to the front of it. After doing that, things operated as expected.

The problem might also arise from differing file permissions, as was my case:

Fresh cloned repository (Windows, Cygwin):

$ git ls-tree HEAD

100755 blob 8099ea496a2c78d71125d79a05855f60ebf07904    testfile

   ↑↑↑

Bare remote repository (Linux):

$ git ls-tree HEAD

100644 blob 8099ea496a2c78d71125d79a05855f60ebf07904    testfile

   ↑↑↑

I had the same problem. Also with a Mac. Looking at the repo on a linux machine I noticed that I had two files:

geoip.dat and GeoIP.dat

Removed the deprecated one on the linux machine and cloned the repository again to the mac. I was not able to pull, commit, stash or pull from my copy of the repository when there were duplicates.

I wanted to add an answer more directed on "Why" this happens, because there is already a good answer on how to fix it.

So, .gitattributes has a * text=auto setting, which causes this issue.

In my case Files on GitHub’s master branch had rn endings. I have dialed up the settings on the repo to check-in with n endings. I don't know what git checks out though. It is supposed to check out with native endings onto my Linux box (n), but I guess it checked out the file with rn endings. Git complains because it sees the checked out rn endings that were in the repo and warns me that it will check in n settings. Hence files are "to be modified".

That's my understanding for now.

I also just had the same problem. In my case I cloned the repo and some files were immediately missing.

This was caused by the path to the file and the filename being too long for Windows. To resolve it clone the repo as close to the hdd root as possible to reduce the length of the path to the file e.g. clone it to C:AGitRepo instead of C:Users DocumentsyyyDesktopGitRepo

Edit file called: sudo gedit .git/config sudo vim .git/config

[core]

    repositoryformatversion = 0

    filemode = false

    bare = false

    logallrefupdates = true

[remote "origin"]

    url = kharadepramod@bitbucket.org:DigitalPlumbing/unicorn-magento.git

    fetch = +refs/heads/*:refs/remotes/origin/*

[branch "master"]

    remote = origin

    merge = refs/heads/master

[branch "productapproval"]

    remote = origin

    merge = refs/heads/productapproval

Change filemode=true into filemode = false

I copied my local repository to another folder and a bunch of modified files showed up.
My workaround was: I stashed the modified files and deleted the stash. The repository became clean.

I found that git was treating my files (.psd in this case) as text. Setting it to a binary type in the .gitattributes solved it.

*.psd binary

I was having a similar problem and found this question.

I was trying to do an interactive rebase, but it claimed there were some modified files, so it wouldn't let me do it right now. I tried EVERYTHING to get back to a clean repo, but nothing worked. None of the other answers helped. But this finally worked...

git rm -rf the-folder-with-modified-stuff

git ci -m 'WAT'

Boom! Clean repo. Problem solved. Then I just had to drop the last commit when I did my rebase -i and finally everything was clean again.
Bizarre!

But I'm adding this solution here so that maybe if I ever run into this again I'll see this and try it. Thanks :D

For new versions of macOS this can be caused by a security feature of the OS.

In the repository I was working on, there was a binary file which had *.app as file type.
It was just some serialised data, but macOS treats all *.app files as an application and as this file was not downloaded by the user, the system deemed it insecure and added the com.apple.quarantine file attribute which makes sure the file can not be executed.

But setting this attribute on the file was also changing the file and it therefore showed up in the git change set without any way of reverting it.

You can check if you have the same problem by running $ xattr file.app

The solution is pretty simple, as long as you don't have to work with the file.
Just add *.app binary to your .gitattributes

Same issue for me. I could see several images with the same name like "textField.png" and "textfield.png" in the remote Git repo but not on my local repo, I was only able to see "textField.png" wich was not used in the project's code.
It turns out most of my colleagues are on Ubuntu using ext4 filesystem whereas I'm on a Mac using APFS.

Thanks to Sam Elliott's answer, the solution was quite simple. First I asked a colleague on Ubuntu to delete the redundant file versions with the uppercase, then commit and push on remote.

Then I ran the following :

# Remove everything from the index.

git rm --cached -r .



# Write both the index and working directory from git's database.

git reset --hard

Finally, we decided that every developer should change his Git config to prevent this to ever happen again

# Local Git config

git config core.ignorecase = true

or

# Global Git config

git config --global core.ignorecase = true