I've been Desktop only for a while, syncing to filesystem to ~/Dropbox/Docs/Frequent Docs/Joplin, a folder I created myself.
I figured I'd get the mobile versions too. I picked Dropbox, but it doesn't let me pick my chosen folder. I get that it syncs into ~/Dropbox/Apps/Joplin instead. I did create a couple of files from mobile that are now saving there and I don't want to lose them.
So... how do I get Desktop syncing with mobile? Do I just copy up all the files and folders inside of ~/Dropbox/Docs/Frequent Docs/Joplin and drop them into ~/Dropbox/Apps/Joplin? I'm cautious because the files look like they have their own format - I don't want to lose data so I thought I'd check first.
This would be easier if I could just pick a folder inside Dropbox to sync to from mobile. Or if Joplin had a tool to move/migrate notebooks from one location to another.
Agreed, unfortunately the Dropbox API does not allow syncing to directories outside of "Apps". So it's not worth thinking about.
There is no officially supported method for migrating folders such as you're doing. That said, you should be fairly safe to do what you described. Before trying strongly suggest you make a backup of your desktop (File -> Export All -> JEX). This won't back up the files from mobile, so I would suggest also making a copy of the files in ~/Dropbox/Apps/Joplin.
If everything goes wrong and you lose notes, you can wipe the desktop files (rm -rf ~/.config/joplin-desktop) and import from the JEX.
If it were me I would do it in the following order:
Export all files from the desktop to a JEX
Move the files in ~/Dropbox/Apps/Joplin somewhere safe
Ensure my desktop is in sync with Dropbox
Make a note of the Help -> Synchronisation status screen
Copy the files from ~/Dropbox/Docs/Frequent Docs/Joplin to ~/Dropbox/Apps/Joplin (which was emptied in step 2)
Change the sync directory on Joplin desktop
Initiate a sync (because the files were moved there is a good chance that Joplin will "sync" all these files, but nothing should actually change).
Check the Synchronisation status screen again to make sure nothing has changed
Copy back the files from mobile (were previously in the Apps/Joplin directory)
Sync again
Check the status screen a third time
Done
The most important thing is to take backups before you start. Good luck!
If you've been using encryption then it won't be this simple, let me know and we can attempt to sort it out.
