I\'m using eclipse egit with github. I found something strange that I didn\'t change anything, but egit marked the file as "changed". See the images:
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