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.NET assemblies that contain a mixture of managed and unmanaged code cannot be ILMerged with other assemblies.
How can I verify if a given .NET assembly contains purely managed code, or a mix of managed and unmanaged code?
Run the PEVerify tool against your assembly.
PEVerify.exe is installed along with Visual Studio, e.g. this one comes with Visual Studio 2012:
C:\Program Files (x86)\Microsoft SDKs\Windows\v8.0A\bin\NETFX 4.0 Tools\PEVerify.exe