There is nothing changed, but eclipse egit marks the file as changed
One of the first things I've had issues with in Git.
I've said this forever:
git config --system core.autocrlf false
To get rid of CR highlighting in diff and patch views, use:
git config --system core.whitespace cr-at-eol
If you share your computers with others, replace '--system' with '--global'.
As a follow up, as I just ran into the same issue, another reason for EGit detecting all files as changed is a POSIX file permission problem at least when used together with Cygwin's git.
The following will fix that; however keep in mind that this also means that they are ignored then:
$ git config core.filemode false