Geoff, here's my 2 cents, with the big caveat that I only briefly looked at the Autoware repo yesterday, so this is more general feedback than specific to your repo.
First thought - you mentioned safety critical code.. I would think you would *have* to separate that into a separate repo if you ever want to get through a safety certification process.
Second thought - I agree that 131 packages is too many for a flat repo like we have for navigation2. In fact I feel nav2 is hitting the limit (I think we're at 27-ish packages now). I'd like to decrease ours and keep it below 25. At some point between 25 and 50 I think you hit a threshold of too many. That's a complete judgement call though.
Third - Given the above, I would look at potentially breaking it into 3 repos, one for the safety critical code that you want to get safety certified, one for perception (as you know, this is common in ROS packages already), and maybe one more for the other core functionality. I don't think messages have to be split into their own repo as long as they're in a "autoware_msgs" package that can be imported as a dependency independently of the rest of the core. I don't know if that's exactly what you're proposing, but that seems like a good middle-ground approach.
Also, as you're doing that you can fix some of your directory naming and heirarchy as needed.
Again, just my general thoughts on the subject, take with a big grain of salt.
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