Fix nested directory xrefs in combined PDFs

[erilot]

All links between pages work, regardless of directory structure and nesting, from any level to any other level.

Note that this works, but I did it under fire and under deadline and wasn't thinking about nice code, so I probably messed up your organization and file grouping. Please make sure it's up to standards. Happy to revise/edit per your guidance.

Couple of other notes:

• There is a hardcoded reference to the site directory in plugin.py which should be pulled from the config instead, but I couldn't figure out how to make that work and ran out of time. It is commented in the file.
• I added a console print statement that provides feedback as to which page is being processed as some of these runs take a long time (90+sec for our docs). This is unrelated to this issue and should have been committed separately. Whoops.