CMakeProject: Handle subdirectories with different defines/include paths

While we do know all the parts, we don't know to which part each file
belongs. So we guess that based on file system proximity.

Task-number: QTCREATORBUG-12359
Change-Id: I9d2a2ca0171b4e43f4a65d2f4b7b318f4e8b451c
Reviewed-by: Daniel Teske <daniel.teske@digia.com>