After upgrading Eclipse from Helios to Indigo with EGit plugin 1.0.0, all my projects seem to have lost their metadata about their git repositories, respectively.
In my case, the git repos existed but the team context did not show the "Share this project" option. It looked like the project was partially configured with git.
I could fix the problem by deleting the project (without deleting the actual files) and then importing the project back to eclipse.