No, occ encryption:decrypt-all does NOT decrypt files in files_versions, files_trashbin, or files_trashbin/versions AT ALL. This is an unsolved problem that was originally reported more than four years ago, and there hasn’t been a solution or even any meaningful guidance in the time since.
So this is the underlying problem I have been trying to solve, and it will require some level of scripting and/or database administration that I am not entirely comfortable doing because I am not an experienced Nextcloud developer. I don’t even know if there are proper interfaces to do what I want/need to do.
btw, I have already reverted to decrypting user by user, and it’s still painfully slow. At the rate it is going, it will take another two months (!!!) to decrypt. I cannot possibly be offline for that long. It’s not even a huge amount of data. The php cli scripts from the recovery-tools are much faster, but they are also designed to work outside of Nextcloud.
As for my question about bootstrapping, forget about encryption for a moment. I am just asking about the general case.
Say I have a basic Nextcloud installation where some basic apps are installed, e.g. files, activity, notifications, etc.
So I can use occ to perform tasks from the command line like occ files:scan, occ activity:send-mails, occ notification:generate, etc.
Now say I want to bootstrap a custom php cli script called custom-occ which will also be executed from the command line.
But I want to be able to specify a different set of apps to be bootstrapped for this custom-occ php cli script, e.g. only the files app from the main installation and a custom app myapp.
So in this case, I would still be able to perform tasks like custom-occ files:scan and custom-occ myapp:function, but custom-occ activity:send-mails and custom-occ notification:generate will not work since they are intentionally not bootstrapped.
I think this would be possible by using an alternate config/config.php, but I am not sure if there is a better way to do this.