(Inspired by @mewltn's comment)
After telling Orion to "always" or "never" allow a website to open a certain application, it should be possible for the user to change their mind in the future.
I imagine this would fit nicely in the 
menu, as it's conceptually similar to the other permissions settings for e.g. microphone access.
I mean, presumably when you select “never” or “always”, Orion sets that preference somewhere. It should be possible to unset that preference? It seems really weird to have a preference that can’t be changed once set!
If you mean “how would that work” in terms of UI, then I guess I’d put it two places:
menu, it could say something like “Open ‘App Store’: [Always Allow]”, and you could click that to change to Ask or Never (just like the other permissions).If you mean “how would that work”
Exactly what I mean 
At the bottom of the website’s
A website may theoretically open unlimited number of different external apps.
In Orion preferences, there should be a place to see all of your saved website permissions — for this as well as other permissions that you’ve altered from the default.
Not clear how would that work as there are two 'axis': one is the domain and the other is apps.
Vlad Well, how is the preference remembered/identified? Why can't the browser simply add entries to the permissions list in the form of "Open [appname]" for each app that wants to open that the user has stored an "always/never" preference for (which is variable but certainly a finite number)?
In the gear menu, there could be a divider below the standard permissions settings, and then list any apps that the user has said the website may always or never open.
Vlad Not clear how would that work as there are two 'axis': one is the domain and the other is apps.
Now I'm thinking maybe this should be split into its own suggestion, but there are a couple ways you could handle this.
The way Brave does it is to have a list of all websites with any kind of stored permissions, and you can click on each one to see all of the saved preferences.
With this setup, you could add the saved settings to the end of the list, just like the gear menu.
Alternatively, the Safari paradigm is to have it organized by permission, so you can see for a given permission what websites have access to it.
In this kind of setup, you could have a section titled "App permissions" or something to that effect, and the list could be organized similar to the App Shortcuts section of macOS Keyboard preferences: for each website with stored app permissions, list all of the stored settings below the website's heading.
