Actually it looks like I was doing a wget of the manual source and untarring.
I've managed to get the includes out of the manual's directory, so I can format it and still do an update without losing the header, css and footer data.
At any rate, the new(er) version is live. I still need to finish a bit on the formating and then do the updates. But at least it's better than the old version.
(I'm on dialup right now, so I'm hesitent to start anythign before the DSL tech arrives to replace my modem)