Makefile.include: fix board/cpu inconsistent include order

Include order for board and cpu was

1. cpu include
2. board include
3. board common includes
4. cpu common includes

Its now changed to:

1. board include
2. board common includes
3. cpu include
4. cpu common includes

Verifications:

There are no common headers names between boards and cpus.
Except native that has a 'periph_conf.h' in cpu instead of being in board.