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When trying to debug in a solution with several assembly references, we cannot step into the code for those referenced assemblies even thought the MDB files are kept along side the referenced assemblies and the build copies those assemblies and MBD files to the debug folder.
For example, iPhoneApp includes references to AssemA.dll and AssemB.dll in a Assemblies folder in the Solution directory, their corresponding .MDB files are in the same directory as AssemA.dll and AssemB.dll (AssemA.dll.mdb and AssemB.dll.msb). In the final build the assemblies and their MDB files are copied along by MonoDevelop but I am still unable to debug in these assemblies.
In MonoDevelop preferences, disable the option to debug only project code. This is the equivalent of Visual Studio's "Just my code" debugging option.