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It's strange to me that Package Control isn't integrated into the core for v3.0, given its usefulness and popularity.

Not yet. I started prepping for the port to Python 3 a bit ago at https://github.com/wbond/sublime_package_control/tree/split_..., but the actual Python 3 changes are still in progress and not pushed (for the sake of not spoiling Jon's surprise).

Has there been any talk about merging Package Control into the app out of the box for v3?

When I tell people how much I love ST2, Package Control is definitely responsible for some of that love.

Probably due to the upgrade to Python 3.

Right. I just figured.

Probably a result of the move to Python 3 for the plugin api?