Transmission

Precisely!

I suspect it has something to do with the beta releases of macOS Safari - specifically the Safari updates and underlying permissions, as you alluded to. maxOS Sierra's Safari has no such problems, while the on going beta releases for the Sierra updates have changed something. Definitely ...

So I spoke too soon...I still haven't resolved getting rid of the "Allow" a magnet link to open Transmission without being asked in a dialogue box. Deleted everything and setup new install exactly like another Mac here - still asks for confirmation. The other Mac does not. Just craziness...why would ...

Deleted all the Transmission directories and plist locations, rebooted, and set all the configurations as I normally have them. Success - no longer have to confirm magnet links. Not sure why it didn't get fixed the first time round, and I can't remember if I rebooted when I first did this. Tho I ...

Great suggestion @x190 - forgot about something as simple as drag'n'drop. Sadly, tho a valid solution, would only be good for a one-off link. Most of the times I've generated a magnet list and go through the list clicking on the magnet links for the stuff that meets my criteria...with the mouse ...

So I managed to fix the infamous adding Torrent/Magnet download, but can't figure out how to eliminate the "Do you want to allow this page to open 'Transmission'? dialogue box. Transmission is running, and this only happens with Magnet links, Torrent links asks for no such confirmation; and I'm ...