to my knowledge monodevelop uses pkg-config to find references.
for nunit two equal ones are provided one from libmono-cil-dev and one from libnunit-cil-dev (one of them should probably be removed, though that does not cause the issue, only duplicate display):
libmono-cil-dev: /usr/lib/pkgconfig/mono-nunit.pc
libnunit-cil-dev: /usr/lib/pkgconfig/nunit.pc
to my knowledge monodevelop uses pkg-config to find references.
for nunit two equal ones are provided one from libmono-cil-dev and one from libnunit-cil-dev (one of them should probably be removed, though that does not cause the issue, only duplicate display): pkgconfig/ mono-nunit. pc pkgconfig/ nunit.pc
libmono-cil-dev: /usr/lib/
libnunit-cil-dev: /usr/lib/