1) Assuming the 'implied' means on-demand from the linux shell and not started by avr_init your data flowchart seems correct except for the fact that although your illustration shows the sqlite and system process dedicated to the tty process, factually any two process in the group can exchange messages.
2) One idea that I'm toying with is a way to have the '32u4 be able to send a request to have
a new sketch overlaid on the current one with a sketch server process.
3) Another idea is to have a program say avr_cron with lots of command line options that can be invoked from shell or crontab
that joins the queue, and messages one of the processes. Lot's of possibilities.
I used the word "implied" because you did NOT state in any certains terms how that would work. I assumed it would NOT be via the sys_init, but beyond that I'm guessing. You did not describe - so I'm just adding words with how of a better explanation.
swapping out one sketch for another would be handy.
You're getting out hand. We you say "Lot's of possibilities." I get chills thinking about "feature creep". You might want to define that, but I can see good ideas coming out of this -- such as a controlled roll over.
But seriously, on #3 the Yun is a fine machine, but with the next two years it's likely to be replaced. As such, ambition has an enemy named TIME
Othewise, I'll be happy to give it a try once you have an Alpha verion.