It was to the point where the working title for Peace Walker was literally Metal Gear Solid 5. Also, Portable Ops wasn't even overseen by Kojima. It is in canon, but the only references to it are a very obscure piece of data in MGS4 that retcons a massive plot hole Portable Ops makes, and a line in Peace Walker telling you to forget about the events of Portable Ops. It's not part of the main series. Peace Walker is.
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^Poorly disguised anti-caps sig