Removed HintPaths for MonoDevelop/Xamarin Studio references. The project now uses the BeforeResolveReferences hook to find all the DLL files recursively in the MonoDevelopBasePath and adds the directories where the DLLs are found to the AssemblySearchPaths property. The MD references still show up as unresolved in MonoDevelop and Xamarin Studio, but building is successful.

Related: http://www.beefycode.com/post/resolving-binary-references-in-msbuild.aspx