Repair Doxygen build infrastructure

After Gerrit 4430 much of the documentation failed to build, but
silently so it was easily missed; equally missing that several
paths have been missing for a while.

- Correct paths after directory tree changes.
- Doxygen now bails when input paths don't exist.
- Fix up some of the less deranged entries in the documentation index.
- Exclude the LUA tree, its documentation is a mess.

Change-Id: I35e6b433feee5e05bca772d93aa1635c724db734
Signed-off-by: Chris Luke <chrisy@flirble.org>