So, what to do? Unless you really want to get all your app updates through the Mac App Store, you can avoid re-buying your software at present. Most programs still allow you to update to a new version via the application itself (look for a Check for Updates option in the menu or in the application's preferences window).

Really, most applications work the same whether you get them on the Mac App Store or from the developer itself--and those that do differ probably have more features when you don't get them from the store. For example, Bare Bones Software removed a couple of features from its BBEdit and TextWrangler text editors--specifically, the programs' command-line tools and the ability to save files owned by another user--to comply with Apple's Mac App Store guidelines.

It would be nice if Apple provided a way to absorb existing applications, or at the very least allowed developers the ability to discount the Mac App Store versions of their apps for users who owned previous versions, but there's no indication that such an option is the offing, so don't hold your breath.

Ultimately, the state of the market may demand repurchasing some applications--especially if others follow the lead of developers like Pixelmator and Sophiestication, who are shifting their sales to the Mac App Store on an exclusive basis. At a certain point, you will only be able to get updates for those programs via the Mac App Store. But the day when that's true for all your apps is probably still pretty far off.