Delete trailing whitespace in help/Docfiles

Purge on broken links within the (HTML) documentation. This mostly involves
deleting SEEALSO entries (where documentation doesn't exist) but also fixing a
few links.

Also fixed the anchor links in TheoryIndex.html and idIndex.html. In both
cases there aren't any entries starting with the letter "Y".

New and updated bossLib documentation.

Cleaning up mistakes and preliminary docs for bossLib entrypoints.