Fix header dependencies

All of the required infrastructure was present, but there were two
remaining issues:
 - OBJS was not defined (instead ANALYSIS_OBJS, TEST_OBJS, ... were
   defined)
 - The include was done before OBJS could be correctly expanded.
   Fixed by moving the dependency inclusion to the bottom of the main
   Makefile.
No longer build the pdu.c file.

There will be no need for the pdu layer, so we don't need to build it.
It's not removed completely yet, because the current code might still
serve as documentation for a little bit.