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Many developers have their XCode DerivedData folder setup to be relative to the project. If you use CocoaPods, this will likely be how you have things setup (see attached screenshot).
This causes Xamarin Studio to add those files to source control and to the project every time you build. Causing each build with MT to require a git rm -rf Build and a revert of the csproj file.
Created attachment 3951 [details]
screenshot of xcode settings
Created attachment 3952 [details]
Screenshot of Advanced settings
just to clarify, DerivedData is not being synced back, right? It's just the intermediate and project directories, right?
fixed in git master
This bug was marked as fixed for Xamarin Studio 4.0.9, which is currently in the beta channel. Try it out!