We have been bitten by this bug too. git stash -u is deleting ignored files.
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> There seems to a bug in git stash. Subfolders with ignored files are
> deleted if the subfolders themselves are not ignored.
>
> How to reproduce.
> ---
> mkdir TestRepo
> cd TestRepo
> mkdir Ignored
> echo " " > Ignored/Ignored.txt
> echo "Ignored/Ignored.txt" > .gitignore
> echo > File1.txt
> git init
> git add .
> git commit --message="Initial commit"
> echo "Test change" > File1.txt
> git stash -u
> git stash pop
>
> Expected result:
> Ignored/Ignored1.txt is present in the repository. It is either not
> deleted after stash or at least restored after pop.
>
> Actual result:
> Ignored is deleted along with any files in it.
>
> I use git version 1.7.9.msysgit.0
>
> Sebastian Schuberth could reproduce this as well:
>
> > I'm able to reproduce this with git version 1.7.10.msysgit.1 as well as
> > on Linux, so please report this upstream to the git mailing list. Thank you.
>
> Original discussion on msysgit mailing list:
> https://groups.google.com/forum/?fromgroups#!topic/msysgit/FuAh7eXbPSw
>
> --
> Regards,
> Max A. Kiselev
> --