On the cleaning part I was thinking of a script put in rc.local for startup, like something that backups the home folder, create a new one and copy the Signal folder in it again?
On shutdown, I don’t know, it must be related to systemd, and probably unreliable (imagine the VM crashes for any reason). A libxl hook could be more reliable but I had no luck with this and it could be too much work?
On opening file and links, follow this guide:
Off-topic(?): take a look at qubes-app-shutdown-idle, although it’s not what you’re looking for, it will give you the same feeling as a disposable that’s shutdowns when you close Signal.