This is only for hidden items, items with quests attached to them should not be mentioned

Adaptive nanites is in administrative search meeting rooms, 

Scavenging in hr will give you a kick that lowers enemies initiative (it's literally useless 2 of your allies have a better version damage from pounce or precise shot is better)

The janitors closet has an upgrade for ava if you go back for it.

Their is a vending machine in the dining area of every map, it has several essential items, you should visit it every chapter.

Just because it's counter intuitive, A purity play through is much easier if you don't kill the drone. Also Lina, the alternative companion you get if you kill the drone has much better abilities than Ava the drone. However she doesn't remove corruption. 

Make sure to complete the battle in the training area. I recommend doing it after fully upgrading for chapter 2. It gives you the bloodlust ability which dramatically increases your damage. as well as a dexterity and stamina booster

in the squad menu you can set companions to be inactive in combat. I recommend doing this with Victoria on a purity playthrough as without the mistress buffs she can be a hindrance.

The shot gun does less damage than the machine gun when both are fully upgraded their is no reason to use the shot gun EVER once you get the plasma upgrade for the machine gun.

Dexterity is the most valuable upgrade do that first and you will have an easier time gathering resin. Also if you intend to farm resin, I recommend doing it in chapter one for players trying to stay pure and chapter 2 for corrupted players as the advanced fabrication room has a business suit for you that will increase resin gains

I refuse to map the maze. Every room has something interesting in it.