Ignore multiple build directories (used when  cross compiling)
Removed duplicate FindQt4
Remove pthread detection and linking: it's unused
Overhaul common's CMakeLists.txt

* Use automoc instead of a manual list of headers
* Remove Qt4 detection
* Created missing .cpp for .h files (for automoc detection)
* Remove pthread linking
* Forcing -lprotobuf is not needed for mingw; msvc only?