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Is there a way to commit all outstanding changes (modifications and any file additions)?
If I select all in the Navigator and commit with a message, there are still a few items with the “A”.
Xcode (supposedly) does not differentiate between staging and committing in Git. This is so as to provide the least common denominator by way of features between Git and Subversion (and anything else they may add in the future).
Have you verified with the command line or your favorite GUI client that there are in fact outstanding changes? It may just be that Xcode did not properly update the status. I’ve seen this problem in all 4.x versions. It’s very common.