Set Transmission as default program when opening magnet links

Chromium uses the default application.

How to find the default application for a given mime type

# general case
xdg-mime query default <mime-type>

# your case
xdg-mime query default application/x-bittorrent
xdg-mime query default x-scheme-handler/magnet

Changing the default application

# general case
xdg-mime default <application.desktop> <mime-type>

# your case
xdg-mime default transmission-gtk.desktop application/x-bittorrent
xdg-mime default transmission-gtk.desktop x-scheme-handler/magnet

Those commands alter the file $HOME/.local/share/applications/mimeapps.list and/or $HOME/.local/share/applications/defaults.list, which means you can also do the change manually.

For Chromium, when I choose "Don't ask again", Chromium stores the following setting in my ~/.config/chromium/Profile 1/Preferences file:

{
   "alternate_error_pages": {
      "enabled": false
   },
   "apps": {
      "shortcuts_have_been_created": true
   },
   "autofill": {
      "negative_upload_rate": 1.0,
      "positive_upload_rate": 1.0
   },
   "bookmark_bar": {
      "show_on_all_tabs": true
   },
   "bookmark_editor": {
      "expanded_nodes": [ "1" ]
   },
   "browser": {
      "check_default_browser": false,
      [...]

For standard Google Chrome:

1. Close Chrome.
2. In Terminal, paste open ~/Library/Application Support/Google/Chrome/Default/Preferences (and then hit enter)
3. search for "browser":{​ and replace it with "browser":{"check_default_browser":false,

When you start chrome back up it shouldn't prompt you anymore.

Note:

The preferences setting seems to differ substantially between chrome versions. On Chrome-78.0 the setting

"browser":{"default_browser_infobar_last_declined":"13236762067983049"}

seems to work. I assume it simulates clicking the x.