Move commands registry to tree.js from commands.js

commands.js just has math commands right now, no reason it should have
to be included before the other commands files.

Prep for commands/*.js being included in arbitrary order.
latexMathParser uses Variable/VanillaSymbol lazily

So that services can be included before commands.
Organize into commands/, services/ directories
Rewrite architecture overview in README

Describes framework in the same order the relevant files are compiled
in the Makefile, melded with the description of terminology.

Also reword header comment of tree.js to match new description in
README.
Merge pull request #239 from mathquill/refactor.directories

Organize into commands/, services/ directories; document