Do a final clean-up of the doc.

In particular:
Fix any bad links -- do a check.
The links to the JNI spec are known to be bad - change to "latest".
Consistently use "live thread" vs "active thread".
Run an XML checker.
Run an HTML checker.
Changes must be done after May 27th since the "latest" link won't go live until then. But should be done before June 3rd.