I have pretty much strange situation. Working on Windows machine and 
committing to Git Stash.

In my global config I have core.autocrlf=true and there is .gitattributesin 
repo with * 
text = auto

Now here is what I do on clean, recently cloned repo:

>git status #1on develop, no changes

>git checkout -t origin/BRANCH-1 && git status #2
Branch BRANCH-1 set up to track remote branch GPIII-96 from origin.
Switched to a new branch 'BRANCH-1'
modified: A.java
modified: B.java
modified: C.java

>file A.java
A.java: ASCII text, with CRLF line terminators

>git rm --cached -r . && git reset --hard && git status
# On branch BRANCH-1
nothing to commit (working directory clean)

>git checkout develop -f && git status 
modified: D.java
**WTF???* **#remember on #1 it was OK*

>git checkout BRANCH-1 -f && git status 
modified: A.java
modified: B.java
modified: C.java

I am really not sure if it is connected to line-endings. I just have no 
idea how to check it.

Any ideas on what's going on and how to fix that?

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