[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.
likewise, I don't see much value in separate Development, Build and Run sections when there isn't that much content. If providing a minimal template, I'm happy just suggesting a "Development" section with notes that the copier should discuss briefly how to develop in this repo.