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Commit 496d1cc8a98efeeb62ad2fd408f4de2aebf4849e in the monodevelop tree works around an issue whereby local copy references trigger unnecessary rebuilds. The gist of the problem is in the commit message which I've copied here:
Xbuild does not handle local copy correctly which results in unnecessary rebuilds. The bug appears to be that if Foo.dll is considered to not need a rebuild, any references which are specified as 'Local Copy' are copied anyway. The result is that the mtime on those changes which somehow triggers a rebuild for other assemblies/projects depending on Foo.dll.
In this specific case, ICSharpCode.Decompiler was local copying some assemblies which triggered MonoDevelop.Ide to rebuild every time, which in turn triggered every assembly depending on MonoDevelop.Ide to rebuild.
This was actually triggered by a bug in the monodevelop makefiles which i knew about and committed a fix for right after I reported this.