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The Mac App Store now includes operating system updates, such as required software patches. These come from Apple directly, while other applications -- such as those that you have bought -- also appear here. It's an all-in-one center for all of your apps and updates.
Messages is a new application that stores all of your iMessages and text messages on your iPhone or iPad. You can take a photo from your iPhone, send it, and see replies on your Mac. You can also send location data and photos.
As you would expect, it also does good ol' fashioned instant messaging and text messaging -- or "legacy chat" -- as Apple calls it.