Update (6/14/13).-- I got a response from Devon Technologies. They indicated due to the rules for the Apple App store they're not updating apps there anymore. They sent me the instruction to convert the apps to the versions available Website, but beware of two things.
First, the Website apps aren't necessarily the same since they're updates to non-App store version which may not comply with Apple's rules for applications and the store. It's the former which is important as you may get error messages for sandbox rules violations.
Second, the Apple App store may get confused with their version and your version to show updates are available for this to return to the older version. I haven't tested these two things yet as I haven't converted my version of the apps from the App store version to the Website version.
Original post updated.-- I've written about my anger with companies who sell apps through the Apple App store but then don't update or upgrade them through the store but only through their Website. I run between 4 and 6 apps waiting for updates through the App store, some going back to last fall.
Well, I'm down to 4 right now, but 3 of those are from one British company, Devon Technologies, which offers a number of apps, some free, but it seems all have updates through them but not the App store anymore.
The fourth one, Timer Utility by JR Productions, is one the company sent me an e-mail they don't intend to issue updates through the store for small changes, but then they don't honor Apple receipts to convert the license from the App store to their Website.
This is ok with me for now as it's in version 4 and I still use version 2 which has a clock. Versions 3 and 4 don't have a clock. I like the clock when I'm not using the timer or other features with the app.
On top of that, the app store doesn't let you completely remove apps, even though some of them aren't offered through the store anymore. In the list of purchased apps there are a few which aren't available in the store anymore but you can't remove them.
You also can't stop requiring updates to apps you hide or don't want anymore and even have removed from you Mac. The App store still wants to download or update them, you'll always get the little flag showing app updates available and the Saturday morning notice you can't stop.
The reason for this is the app Tiny Alarm by Plum Amazing. The completely redid version 1.6 which was a cool, simple to use, timer to version 1.7 which is full of bells and whistles to be bloated for using it as a simple alarm clock. And I don't like the way the app signals the end of the time set in the alarm.
So I run version 1.6 under a different name but the shared files with version 1.7 tells the Apple App store I need an update. So I update it which overwrites version 1.6 with version 1.7 and after closing the App store app/window, I copy a backup copy of version 1.6 to overwrite the updated version.
All in all the app store is a good idea, it's just been badly managed by Apple and badly treated by app companies. Furthermore I hate updating Apple apps through it, I like the old separate update method. But I can't change that, but sure would like Apple to give users more control over the apps they have in the store.