EGit showing directory as always dirty

Question

I started using EGit with eclipse and one of my directories (which contains many submodules and regular directories) always shows as dirty. I have tried to git reset --hard and re-create the project from scratch. If I select the directory and Compare With git index or HEAD, it does not show any changes.

If I use git on the command line for the folder, git status does not show any pending changes and git submodule lists all the submodules correctly. Using EGit, I tried to set the Assume Unhanged option. But this propagates to child directories too (which isn't desirable).

I am using Eclipse 4.2.1, EGit 2.1.0, and Geppetto 3.0.0. What else could cause this directory to always show as dirty? Any way to just ignore changes to this directory (but still changes to the siblings)?

Update - Oct 2nd, 2013:

• There is a feature request open to support this at https://bugs.eclipse.org/bugs/show_bug.cgi?id=391280.
• From comments, it looks like a submodule might be considered a symlink and the work being done to implement this support is at https://bugs.eclipse.org/bugs/show_bug.cgi?id=354367.
• Gerrit branch information for the work being done is at https://git.eclipse.org/r/#/q/status:open+project:jgit/jgit+branch:master+topic:symlinks,n,z.

Update - Sept 24th, 2014:

• There is an additional umbrella bug at https://bugs.eclipse.org/bugs/show_bug.cgi?id=429304 that can be followed for the issue specific to EGit.
• I no longer use Eclipse or EGit and have moved to Atom with the Git Plus plugin. I will try and continue to update this when the issue is fixed. But Atom and Git Plus satisfy me much better now and this issue isn't relevant to me at the moment.

Answer 1

It could also be due to differences in line-endings between the multiple people who have pushed to the remote repo, the remote repo (usually bare, but OS-specific line-endings), and your git settings. Is this something that you can verify?