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I have a VS2008 solution with two C# projects. Both projects refer to external libraries (assemblies) which are located in a sub-folder (e.g., "../third-party/Foo.Bar.dll"). These references have paths in their Include attribute:
<Reference Include="../third-party/Foo.Bar.dll" />
but MonoDevelop displays this message for each of those references:
Assembly not available for Mono / .NET 2.0 (in Mono 2.10.9)
MonoDevelop cannot build the solution; however, the solution can be built on the command-line using xbuild. Also, the solution can be built using Visual C# Express 2008.
If I edit the two project files and change these references to replace the paths in their Include attributes with HintPath elements:
then MonoDevelop doesn't display the message above, and it's able to build the solution.
Not sure if this is a bug, or simply a known limitation.
MonoDevelop now uses xbuild to build projects, so this should not be an issue anymore.