Move include and source files to logical locations

Move almost all system include files to a logical sub-directory
under ./include. The only remaining system include directories
not under ./include are specific to the platform. Move the
corresponding source files to match the include directory
structure.

Also remove pm.h as it is no longer used.

Change-Id: Ie5ea6368ec5fad459f3e8a802ad129135527f0b3