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This is not really a big deal, just a trivial annoyance.
When first opening and then saving a (.csproj) project in monodevelop that has a <ProjectReference> the casing of existing guid inside <Project> element will be forced to upper case.
Visual Studio 2013 saves the guids as lowercase, so fixing this will reduce noise in source control.
I created a branch and pull request to fix this here.
A fix will be included in XS 6.0.