Software Update to Move Inside Mac App Store in OS X Mountain Lion
Apple's Software Update has long been the primary method for users updating their systems, with the tool accessible through the Apple icon in the menu bar offering automatic weekly checks for new software updates from Apple. But as shown by iClarified, Apple is doing away with the standalone Software Update tool in OS X Mountain Lion and integrating it directly into the Mac App Store.

Pocket-lint has more on Apple's decision:
Currently Apple's Software Update system in Mac OS X 10.6 Snow Leopard, and Mac OS X 10.7 Lion force users to use a dedicated update procedure that constantly checks to see if updates are available. Apple now feels, it seems, that this way of doing things might be slightly confusing to users coming from an iPhone or iPad who are used to seeing updates for apps appear in the App Store rather than buried elsewhere.
Explaining to Pocket-lint in a behind-closed-doors briefing for the new developer preview of Mac OS X Mountain Lion, Apple has told us that the new method will offer updates to the OS and Apple applications in a similar way to how it does on iOS via the App Store, but in this case via the Mac App Store.
The report notes that the move appears to require that users sign up for an Apple ID if they have not done so already in order to access the updates, and also encourages them to keep the Mac App Store within easy access in their Docks so that they will notice badges informing them of available updates.
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