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pkg-config

Gentoo Mono Handbook
.pc-files
MonoDevelop does not look for assemblies in the GAC.
On Mac and Linux, MonoDevelop uses pkg-config to locate installed packages and get the list of assemblies that each package provides.
A package specifies this list of assemblies in a .pc file which has to be installed in the standard pkg-config directory.
http://www.monodevelop.com/help/faq/
http://stackoverflow.com/questions/8980105/monodevelop-compilation-gac

If you are developing a library, MonoDevelop can automatically generate a .pc file for your project (in the project options dialog, select “Linux Deployment Settings”, and check the “Generate .pc file” option).

which part of Makefile.include installs the .pc files?
not everything uses that Makefile.include
that is what MonoDevelop auto-generate
with the LINUX_PKGCONFIG var
so patching the path in that include file should do the trick