The only change in Libmarpa relevant to the theory paper, which is very high level, is that described in the
"engine rewrite post" that you link to. At this point, I have trouble remembering where everything is, so I'm glad you found it.
The /work/dev/{marpa.w, api.texi} in the Github repo contains the very latest work. My policy is to update comments, and whenever I make a change I look for those places likely to be affected & fix them. Also, whenever in re-reading I find an error I fix it, and many in the Marpa community report errors to me, which also get fixed. To get everything, it'd be necessary to reread the entire
documentation carefully from beginning to end and that I have not done in some time, so at this point
errors have probably accumulated.
One minor note, I often use the phrase "as of this writing". When I use it in an doc intended to be permanent, it's a warning to the reader that the situation might change without the doc catching up.