Makefile.inc1: clean up stale dependency hacks

Our dependency tracking cannot directly cope with certain source tree
changes, particularly with respect to removing or moving source files or
replacing generated files. We have a collection of ad-hoc workarounds
to handle these cases. As there is a (small) build-time cost inherent
in these workarounds, we do not want to keep them indefinitely. Thus,
remove workarounds from 2017.

Sponsored by: The FreeBSD Foundation