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manifest for "Make Project" module is not generated by NB's build harness, it's hardcoded. This cause some maintaince problems, i.e. after update Properties->Libraries dependencies module could fail on startup, because manifest doens't contain new dependency. Module "Make Project" should be updated to be "fair" NB5 Module Project
I've checked, "Make Project" doesn't have described problems. It's manifest is autogenerated. Sorry for confusing. I close this issue. (http://www.netbeans.org/issues/show_bug.cgi?id=75155 is still valid)