I have been using Egit (in Indigo) recently in Linux and I have a problem with project explorer/staging view wrongly showing files as changed (in unstaged changes) even though I have not done any changes to the files after cloning a repo. I check the git status in command line (and even in git gui) and it also shows no changes to files.
Has anyone else experienced this problem? What could be a problem? Is it a bug or something specific for my case?
If your team also includes developers using Windows, you could be running into a linebreak/core.autocrlf issue that was present in some earlier versions of EGit. Usually running 'git status' and then refreshing the Eclipse workspace will make these spurious differences go away. I'm pretty sure this problem has been fixed as of EGit 2.1. I know I haven't seen it for some time.
If everyone on your team is using Linux (or OS X), then this is some other problem I haven't seen.
Either way, you should consider upgrading your Eclipse to Juno SR1. Or if that's not feasible, at least install EGit 2.1, which is the current stable release, or 2.2, which the nightly-builds release. The nightly builds are of course a little riskier in theory but I've never run into any problems in practice.