header-comp: Fix duplicates deletion
Irony: Rewrite flags management use one main variable irony-compile-flags.

- extra-flags + include-dirs are no longer differentiated
- pkg-config is removed
- -working-directory is added
- irony-header-directories-root has been replaced by
  irony-compile-flags-work-dir
- now header search paths are retrieviable with the function
  `irony-header-search-paths`, they deduced from irony-compile-flags