First, can you upload the jupyter app info to https://git.cloudron.io/cloudron? It seems to be missing.
The name is a bit different since it's based on the upstream hub project - https://git.cloudron.io/cloudron/jupyterhub-app
Are the rest of the questions somehow related to Jupyter? I will try my best to answer them but I am missing the context. If you can give me the use case for each of the questions below, I can help further.
Is there some good way to just flag certain directories as to be preserved?
Only /app/data is preserved. Even symlinking won't work since the backup logic does not follow symlinks. So far, we are yet to encounter an app that cannot be covered with a single directory.
Can we create our own addons? How hard would that be?
addons are part of the platform. they are not hard at all, they are just docker containers with a "service" API. But they require quite a bit of work and testing. What new addon are you thinking of?
Could a modified version of "proxyAuth" let you spin up separate per-user instances of an app?
I think I understand what you are asking for. For example, there are some "single user" apps. Would be nice to somehow spin multiple instances of these "single user" apps. IMO, would be best to somehow make those apps multi-user 😉 Given most of the apps are opensource, time can be spent contributing upstream. A workaround is of course install an instance of an app for each user...
Is cross-app file sharing a thing? Something like a shared mounted drive?
See Voilumes. You can create a directory on the server and create a volume. Then this volume is mounted into any number of apps you want.
R