Real quick... I recently switched from Eclipse to IntelliJ, and one thing that's been annoying me is that IntelliJ keeps putting the src\main\resources folder of my Android project into its list of source folders. Removing it only helps temporarily; it gets restored again later (I think when I build from the "maven projects" window). Solution: exclude this folder at the compiler level, in the project settings. File->Settings->Compiler->Excludes.
Credit for this solution goes to Sergey Evdokimov, who posted it here.