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When compiling a project that has a strong name, MonoDevelop will check that all referenced projects have a strong name, and otherwise abort compilation.
This is of course logical, but it differs a bit from what Visual Studio does.
In Visual Studio, the reference strong name check is done when a type is actually referenced inside the project being compiled.
As the project I am working on loads the assemblies at runtime, there is no need to check the strong name (and some projects have references that are not strong named). With Visual Studio, I can reference the projects without actually using them in code. This causes VS to copy the dll's into the project output folder, where I can later load them dynamically.
With MonoDevelop, I can not compile the project which references the projects that are not strong named, and thus the dll's are not copied to the output folder.
I realize that this is perhaps a slight abuse of how the build system works, but I have not found any alternative way to achieve the same with MonoDevelop or VS.
As a workaround, you can add the assembly as a file to the project, setting the build action to None and the Copy to Output Directory option to Always.
That does not really work, because the file to copy depends on the type of build, i.e. you cannot add both debug and release files to the output folder.
Also, any dependencies must be manually included as well.