I've contacted Valve to switch the game from free to paid, as well as include the Episode 3 package out of the box.
People who got the free app before this should be getting Episode 3 for free. Consider this my attempt at course-correcting after the confusing mess that was release. Yes, it's extremely unfair to those who paid for the games, but it's the least bad outcome I can make out of my gross mistake. As far as I can tell from here, anyway.
Episodes 1 and 2 are still there for completeness' sake, but will remain DLC as they aren't quite essential. Nor very good.