[doc] TOOLS-594 eng update README.md.

- `rm server.js`: stale worse than nothing.
- Sub-headings markdown.
- Added sections based on what's used in real Joyent repos
  including renaming "Repository/Directory" section to "Code Layout".
Restdown content *is* Markdown, but also gives us a TOC and some controls over styling (with the restdown "brands").  In any case, moot because we're dropping this section. The eng guidelines doc mentions this is restdown, so fine either way.