But the problem can go beyond simple confusion. Though you might be inclined to think that the store has found all of your existing apps and "grandfathered" them into the store, it doesn't mean that you'll be able to get updates for those applications via the Mac App Store itself. And what about those third-party programs that you have installed that don't show up in the Mac App Store? Do you have to repurchase all of those?
While there's no simple answer to the dilemma, let's take a look at the underlying issue that causes this confusion, and then see what you can do about it.
Bundle, bundle, who's got the bundle?
The culprit here is something called a "bundle ID." This is a unique identifier, created by the software's developer, for each application on your computer; the system uses these IDs for storing settings and other information. They look a bit like a Website address in reverse: iTunes's, for example, is com.apple.iTunes. If you look in the Preferences folder inside your home directory's Library folder, you can see the bundle IDs for most if not all of the programs on your computer.
The problem arises from the fact that when the Mac App Store was announced, Apple didn't tell Mac developers who wanted to put their wares in the store whether they should use the same bundle ID for the Mac App Store version that they use for their existing app or create a separate one--never mind that the two versions of the software may be, for all intents and purposes, identical.
When the Mac App Store launches, it apparently scans your computer for a list of those bundle IDs, which it likely pulls from a centralized OS X system called Launch Services. (You can pull up the list yourself with a little --scroll down to the comments for the most recent version of the command).
If the store detects an application installed on your system where both the bundle ID and the app's version match the information associated with the app for sale on the store, that app gets marked as Installed. Those are the apps that where the developer chose to use the same bundle ID for the version in the Mac App Store as the one that it sold elsewhere. (Note that those apps do not show up in the list of Purchases that you can access in the Mac App Store.)
Red Sweater Software founder Daniel Jalkut told me via e-mail there are pros and cons to each approach. The problem in the first case, he says, is that users may believe that--because the app is already listed as Installed in the Mac App Store--they'll be able to get updates through the store, write reviews, and so on, even though that isn't the case.
However, apps that use a different bundle ID for their Mac App Store version present separate challenges. In that case, as Jalkut points out, the store will still show you the option to buy applications that you've already purchased elsewhere, potentially leading to unintended double-purchases--a risk exacerbated by the fact that the App Store has trained most users that they can re-download an app for free and because the Mac App Store doesn't currently ask for confirmation before a purchase.
Seeing double
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.