Makefiles need a cleanup pass

[gdt]

There are many little issues, most of which aren't too serious, but the entire makefile world would benefit from comments, removal of things that are no longer relevant, simplification, etc.

Before really starting on changes, we need a specification of the build environment and what the build system is supposed to do. This is complicated because of optional UIs, doc build, building native packages for mac and windows in addition to POSIX builds, and probably other things I am not thinking of.