build: Make changes to scotch build permanent.

Every time you configured with internal scotch, you'd get modifications
to its Makefiles which git would show as modified. This is troublesome
whenever you want to commit or change branches, because you'd have to
remember not to keep those changes.

The changes to the scotch Makefiles are independent of any options you
might pass to configure (except that they aren't done if you aren't
using internal scotch). We can just make them permanently in git,
especially because the changes have been made upstream in scotch as
well.
build: Remove backup Makefile targets.

These commands are a relic of a non-distributed VCS. Now, if you need to
backup your work, just make a commit. No-one else has to see it, but
it's a lot safer that way. And if you don't want to go through the
trouble of a commit, just run `git stash` instead.
build: Remove unnecessary creation/deletion of directories.
Cleanup C code slightly.
build: Remove extra build script.

There are already makefile rules for these programs.
Remove duplicate constants.h file.
Correct licence in several files.
Remove todo file after moving issues to GitHub.
Remove commented code for absorbing boundary snapshots.

It was commented out almost 3 years ago; I don't think it's going to be
reinstated any time soon.