redo include path logic for pre-generated headers

make the include dir in the source tree the "main" include path, as
that's where the majority of the headers is. then selectively add the
shadowed dirs.

Change-Id: I03ad13cfcf77175c141b94d41b1221740d851faf
Reviewed-by: Joerg Bornemann <joerg.bornemann@digia.com>