You can open the ships and bases window and select the top item, then hold shift and select the bottom item, then press Retrofit. Or you can select the category first, if you want to just retrofit a specific category of ships/bases, etc.
Yes, but that's what I meant "without manually ordering each ship or fleet to retrofit". Giving a direct order to ship or ships s a bit different from I seem to see the Advisor command doing. If I'm not mistaken, when I order a retrofit through the Advisors' advice, it queues a retrofit command to the concerned ships, then puts them back on auto. It's way more work finding the ships and then doing the same by hand.
So I'd like to either find a button that does this, or be able to recall the previously dismissed advice from the chat log.