I migrated from Joplin to Obsidian a year or two ago. It was straightforward. With Joplin, I had to use the export functionality from the desktop app. That cleaned up any non-standard bits and allowed for a straightforward import into Obsidian.
Recoll (thankfully) has a GUI. It isn’t the prettiest app, but it was easy to set up and I’ve otherwise quite happy with it.
I have had the exact same issue as you. Thunderbird is great, but their attachment search is not. I spent a lot of time looking for a way to make it work and what I settled on is using a third party program to serve this function: Recoll (https://www.recoll.org/index.html).
It should be available in your distro’s package repository.
You’ll need to download your messages to your computer, but it will work in the way that you expect search to work (I.e. search by filename, search by text within attachments, search by text within emails). Setup is straightforward. You just need to point it to the Thunderbird profile directory where your emails are saved. As a bonus, you get good desktop search for all the other files on your computer too.
Sadly (don’t throw anything at me), the only desktop email program that I have found that does search properly is Outlook desktop. On Linux, that is obviously a non-starter.
Seconding Bookstack. I’ve embedded videos in it and I don’t recall anything special to do it. I also think there’s a way to comment on specific pages…mostly because I remember disabling that functionality.
Agreed on the roles and permissions aspect though. It’s pretty standard to do that for bigger deployments, but it may be a bit overkill for a single user instance.
Are updates being done by the OS automatically or are you going into the terminal and running an apt-get upgrade periodically?
I’ve had issues when I do a terminal update because I believe that Pop expects you to do an apt-get dist-upgrade