When an app/program is not from an authorized developer, it cannot be opened directly because of security settings.
These security settings can be overridden by adding the app as an exception to the security settings, or by using the "open anyway" button in the security & privacy settings page.
Where can I see a full list (with complete paths) of all apps/scripts that were ever added as security exceptions in this manner? I suspect a previously "allowed by me"/installed app to be dirty and need to check.
scutil --list
because that will list all the events that Gatekeeper encountered; both "allow" and "deny". Unfortunately, all the apps are hashed, so it will require some investigative work.