[BUILD] added clang warnings as suggested in #652
[INTERNAL,BUILD] restructured include_directories calls

 * we now distinguish between internal and SYSTEM includes and instruct the compiler to ignore system includes
 * note that everything that doesn't come from the current package will be treated as system (e.g., OpenSwathAlgo is SYSTEM from OpenMS' point of view)
 * renamed include directories variables to match the name of the corresponding target (preparation for export stuff)

I additionally removed an unused CMakeLists.txt file from openswathalgo
[NOP] fixed a couple of unreachable-code warnings
[BUILD] reduced number of warnings by disabling doc related warnings

 * -Wdocumentation-unknown-command
 * -Wdocumentation