Feature/config and options documentation

@brutski Please review and merge.

This PR consolidates and restructures documentation and fixes some YARD issues.

It does not need to be review for content as a future PR will contain pertinent edits. Wanted to get the broad strokes done to make it easier to review the actual edits to content in a future PR.

Only merge after merging: https://github.com/mdsol/crichton/pull/181
I think "[protocol name]_ protocol_" needs to be somehow escaped. It is rendered as [protocolname]protocol (with protocol being italic type)