document `timeout` and clean up

CONTRIBUTING.md
- document `timeout` tag
- reorder tags in frontmatter doc
- minor cleanups
- minor fixes
- add style note
- reformat flags
- remove discussion of obsolete $INCLUDE
- incorporate line notes from @domenic
- integrate additional comments
- add links back, move arg notes down
- Raise outline level by one

README.md
- link to CONTRIBUTING
Merge pull request #89 from smikes/CONTRIBUTING-document-timeout

document `timeout` and clean up