Edits to move all outputs to the output directory + HTML bugfix

The webBook is now in `output/webBook`.  The pdf and tex files are now in `output/`.  Comments were updated to reflect these changes.

HTML fixes in TOC:
- Links to top levels of chapter (i.e. intro.html) were not complete paths
- Tags added to chapter URLs to allow view to jump to a specific header weren't working.  There were spaces in the tags added to the URL - removed them.