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The manual is available here: https://steamcdn-a.akamaihd.net/steam/apps/559100/manuals/Phantom_Doctrine_Official_Manual.pdf

It's a rare thing for devs to release a decent manual, so this is cool.

Note that it doesn't currently appear in your extras tab in GOG (I assume this will be added shortly?).
In the works:
https://www.gog.com/forum/phantom_doctrine/pd_manual
It's available now with your downloads.
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IFW: It's available now with your downloads.
Sweet. Hope patches come this quickly (Steam already has one).