I prefer to programmatically move notes between directories with a script. This allows me to automatically refile notes containing certain terms or select the desired directory with fzf. If I do this, however, the links inside of my notes break because Obsidian is not aware of the location change.
I would love to see a feature added to Obsidian allowing the user to move files with a command line option (or possibly a specialized URL scheme.)
That way, users could write scripts to refile their notes, and Obsidian could keep the links up to date.
Here is an example of the kind of workflow this script would enable.