Ok, here they are:
https://puredata.info/Members/jwilkes/PDDP-help-patches/view
To use them you can just overwrite the doc folder with these changes.
After doing that you can open the <ctrl>-b browser and there's a
search-test.pd prototype at the bottom.
I put headers and a "pd meta" subpatch in 2.control.examples, 3.audio.examples, and 4.data.structures, and changed all the 5.reference files to conform to the PDDP template (nonrecursively!).
To find patches that obviously still need work, try KEYWORD needs_work.
For the tutorials I moved things around but did not mess with any wires, so they should all work as they previously did.
One _big_ problem currently is the bug in pddplink that breaks abstractions and other links if you go down a relative path. Also I couldn't use pddplink for the manual because relative links for non-pd files don't work.
Also, if anyone wants to tweak pddplink, I also put in a feature request
for a flag that would close the original patch once you click the link.
That way you can add some simple navigation links for some of the tutorials.
Let me know what other revisions need to be made, and I'll implement them (I'm not totally burned out yet!)
-Jonathan