I'm at Unity 5.6, and this problem has been going on since 4.3. Sometimes, suddenly, MonoDevelop sees two copies of many files, and this is annoying because of this: "Go to Declaration" instead of just going there, expands to two different, identical, choices. Formerly I fixed this by going in the solution options and deleting the "Release" configuration, leaving only the "Debug" configuration. This doesn't work anymore: I deleted the Debug configuration, restarted everything, still duplicate files. Will anyone, after 2.5 years, FINALLY try to solve this problem? I know it's obviously not top priority, but getting ZERO answers for so long is incredibly frustrating.