Nah it makes sense that mer becomes the new base/root dir, maemo 5/6x* are legacy, + they're not low lvl like mer (they're full stacks), they should be a main "branch", alongside nemo & sailfish.
But that probably won't happen with the Hildon Foundation/Council, unless they're willing to work with Jolla & vice-versa, I'd say it's more likely that Jolla will end-up doing something without them.**
I spoke to them again about collaboration recently, they hinted that they have plans for proper community infra similar to maemo.org, but it was a vague response, so I wouldn't take it as gospel yet.

*Maemo 6x AKA MeeGo-Harmattan 1.2 or Harmattan
**and that something most likely wont include any community infra for maemo 5x/6x.