You max out perks by repeating certain combat tasks over and over again. The perks have up to 5 levels. You can farm all of these via checkpoint restart. However, it has to be done in one playthrough (when starting a new game you lose them). You can check your progress at any time in the pause menu. Below is a list of all perks and their upgrade requirements.
Stealth Perks:
Stealth Takedowns: Silently killing soldiers from behind using stealth takedowns.
Enigma Codes: Collecting enigma codes found by searching dead commanders.
Thrown Hatchet kills: Killing enemies by throwing hatchets at the target.
Quick Commander Kill: Killing commanders before they activate the alarm
Takedowns or tampers: Performing takedowns on or tampering with robotic enemies.
???
Chaos Perks:
Heavy weapon kills: Killing enemies using heavy weapons, such as the Hammergewehr.
Grenade kills: Killing enemies by using the Handgranate.
Dual-wield kills: Killing enemies while dual-wielding weapons.
Overcharged kills: Killing enemies while health is overcharged.
Combat Takedowns: Killing opponents using combat takedowns when up close to the enemy.
???
Tactic Perks:
