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When using Team > Commit on a repository created using the Git Sharing Wizard, all files in .metadata are offered for commit. I guess this is because of the new "Commit resources outside workspace" feature... Not sure if the commit code should be fixed or if the Git Sharing Wizard should simply show a confirmation dialog warning to the user that they are sharing their workspace (and what the consequences are). The dialog could also say something like "You should move your projects to a location outside your workpace by right-clicking on "Refactor > Move..." before sharing them. I found this because I'm currently writing a short chapter for the EGit user guide describing recommendations for exactly this kind of problems. I'll post this chapter sometime soon for feedback.
*** This bug has been marked as a duplicate of bug 332834 ***