Bug Fixes:
* Fixed missing variable replacements.
* Removed hard-coded host names from configuration file paths.
Documentation Features:
* Allow command-line length to be configured using cmd-line-len param.
* Added compact param to allow CSS to be embedded in HTML file.
* Added pretty param to produce HTML with proper indenting.
* Only generate HTML menu when required and don't require index page.
* Assign numbers to sections by default.
* VM mount points are now optional.
1) Started on a general markdown renderer
2) Internal links now work in PDF
3) Improvements to PDF styling
4) Some comment and formatting fixes
5) User guide edits.