Correct usage of SYSTEM in Cmake's include_directories

The option SYSTEM to Cmake's include_directories command specifies that all following directories are to be treated as system directories (i.e., passed to the compiler with -isystem instead of -I). However, there were also some ROOTPWA directories after the SYSTEM option. In principle this could affect dependency generation and the level of warnings/errors emitted.

The directories have been sorted, so that only non-ROOTPWA directories come after SYSTEM. For the moment all external include directories have been added after the SYSTEM option. This could be changed again.
One could also think about directly putting the directories to the include_directories command, instead of first defining a variable only used this one time.
It should be tried whether the redefinition of CXX_FLAGS in the cuda directorty are still necessary.