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Created attachment 1423 [details]
Patch to take libdir into account.
MonoDevelop installs things into $(prefix)/lib even if libdir argument is provided on the ./configure line.
In attachment is a patch fixing that issue.
This is intentional, MonoDevelop is not architecture-specific, so it doesn't make sense to put it in an architecture-specific libdir. The same applies to Mono's CIL libraries.
Also, in order to make such a change, it would be necessary to test and fix all the things that depend on the existing behavior.