Turn off autobrief for pages in the documentation, do a pass for naming structure

Here's my suggested fix for the auto brief issue raised in #1150.

What I've done is added a filter that transforms `*.dox` files on-the-fly to use javadoc-style comments, and turned off `JAVADOC_AUTOBRIEF`.  That should mean we can keep doing what we've been doing, and there will never be brief sections in the reference guide, but the API docs will be unchanged.