docs: describe, visualize, and verify internal code structure and layering

Try to describe something that isn't entirely there yet.

deps.py will help track and minimize violations through checks and
visualization in deps.svg .

scripts: handle running with pending deleted files

Don't fail on files in manifest missing in working directory.

scripts: make output from run-all-cleanup easier to parse

Make it clear that it didn't end prematurely due to some invisible problem.

cleanup: run pyflakes as a part of scripts/run-all-cleanup

pyflakes has no usable configuration options, so create a small wrapper script.
Instead of having two wrapper scripts (with one being almost nothing and the
other containing configuration), just keep it simple and use one combined.

run-all-cleanup: fix incorrect interpreter

POSIX (and Debian) requires /bin/sh.