git buggy modified files when changing branches

Question

I have the craziest bug going on with my repo I don't know what to do. In my repo I have three branches.

master > branch_1 > branch_2

From branch_1

git status and all is clear no files are staged or modified.

From branch_2

git checkout branch_2 and type

git status again and all of a sudden I have these two files that are marked as modified

What I've tried

I try to do a git checkout on both these files but they keep re-appearing as modified automatically

Only special setup: The only thing special about these files is that they are part of a git subtree repo within this repo.

What's going on here?

OS windows 8.1

git version 1.9.4.msysgit.0

Answer 1

I would sanity check that you don't have the files open somewhere else on your computer. A code editor may be saving a cached copy of the file in memory. Once you're sure you have nothing open, you can start looking into other options:

• run git stash pop - maybe the files had been stashed at some point with git stash and now it's a few commits ahead and behaving buggy
• you could always try git reset --hard which should throw away all uncommitted changes.

Answer 2

Check for:

• your .gitattributes files in that branch for any core.eol directives, which can change the end-of-line character on checkout.
• the execution bit on those files (which should be reset by a git reset --hard, as suggested in DrewT's answer (upvoted)

Those are the two reason which usually lead to "differences" on a checkout.