- All resources are either under src or under resources dirs
- Removed files top level directory
- Move flightgear files to top level dir

Moving methods from MainWindow to QGCApplication so that more things
can run without a window. Helpful for testing.

Subclass of QMessageBox which re-implements the static public
functions. There are two reasons for this:
1) The QMessageBox implementation on OSX does now show the title
string. This leads to message boxes which don't make much sense. So on
OSX we set title to text and text to informative text.
2) If parent is NULL, we set parent to MainWindow::instance. This
prevents message boxes which can go behind MainWindow

Using QFileDialog directly on OS X can hang intermittently due to Qt
bug.

Fix execution context of thread routines - note that this is not quite the architecture the Qt folks intended, but as they admit its the consequence of their architecture.

Conflicts:
	src/comm/QGCFlightGearLink.cc

Fixing -Wuninitialized