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The current version of the Pathfinder pack does have two magus adjustments in the conferred abilities section, "Magus: Arcane Pool" and "Magus: Spell Combat".
(I'm assuming the "Magus: Arcane Augmentation" one you are seeing is built-in as part of LWD's Inner Sea Magic data file, since I don't see that one.)
Are you sure you have the ShadowChemosh's Adjustments source selected in the Configure Hero options?
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