[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".
If anything I want to drop the dir layout sections from our READMEs. Strong thoughts? Some value, yes, but lots of redundancies there, e.g. "docs/   Thios is for docs".  Well duh. I don't think the extra overhead in the READMEs is justified. Must prefer to have short and sweet readmes. Can we drop this from your PR?