Implement compiler flags and parsing of legacy switches

Other functionalities are now in:
 o -I, -D, -U compiler flags properly percolated to rootcling
 o capabilities filename, no_membertypedefs, no_templatetypedefs
   rise a warning stating they are not supported anymore to get
   feedback from experiments when deployed
 o The other legacy options are swallowed, e.g. the gccxml ones.

Minor improvements, mainly extraction of repeated functionalities
in functions for better maintainability and readability.