Stop the Presses! While not quite completely “operator error”, I believe I found that it wasn’t the AppleScript which only moved items in the Spam folder to the Trash, but that the script wasn’t even being run since my upgrade to El Capitan.
I found that my keyboard shortcut (Control-Delete) for running the script was no longer assigned in FastScripts’ Script Shortcuts; it was showing “(none)” for the shortcut—a change I can only ascribe as an unwarranted side effect to the upgrading to El Capitan. (As an aside, another such side effect was the enabling of e-mail accounts I previously had left as disabled.) So, since the upgrade to El Capitan, when I was selecting all the messages in my Spam Mailbox and doing the Control-Delete shortcut, the script didn’t run and Mail was treating that as just a Delete—don’t know if there were a default action for a Control-Delete—and putting those messages in my Trash Mailbox where they awaited my additional action to delete them from there.
I’ve now restored the Script Shortcut of Control-Delete, the script is run, and all the Spam was completely deleted without any further action by me. (I now suspect even my out-of-date script would have still been doing all the proper actions if it had been run.)
I did the update, but noted that although the text of the script has “Last Modified: 2015-06-23”, when I downloaded the compiled format, it presents in the Finder and Get Info a Last Modified date of 2015-08-19 at 16:16. (I suggest you update your “SpamSieve AppleScripts Change History” thread to reflect the change to whatever is the date of the latest version.)
Please check the Console for any errors that occurred while running the script.
Before installing the updated version of the script, I did check the Console’s SpamSieve.Log.log and didn’t find any errors, but then as noted above, I subsequently found the script was not being run.
Sorry for having raised a false alarm.