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This seems to be a regression. There are now two MEF trees:
The second does not have the fix applied to get it to work on case-sensitive file-systems. It seems that the second is the one that's actually used when I build and install Mono and then try to run an application with --runtime=v4.0.
See also: http://mef.codeplex.com/workitem/10486 (Where it appears the MEF team declined to fix it upstream.)