To get the player upgrades, you will need to find both Supplements and Training Manuals. Supplements are found fairly easily in obvious and not so obvious spots. Training Manuals open up a new part of the Upgrades section of the crafting menu and are mainly found in out of sight spots and in safes, so it will be a good idea to go for the Safecracker and Journeyman trophies for this.
To buy them, go to the upgrade portion of your crafting menu by pressing the PS pad button and pressing

.
Each section of the upgrade has 5 subsections; costing differing amounts of Supplements to fill, ranging from 20 to 60. Once you have enough Supplements, hold

to learn it. If you scour for the supplements, you should be able to get 25 upgrades learned during Abby's story.
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