So, you want to get the 'Mutant' achievement.
Combat on Extreme difficulty can be pretty challenging - enemies take a lot of punishment before going down and can, in turn, wreck you in just a couple hits. Encounters drag on forever, as you're slowly chipping down their HP, while constantly watching out for attacks.

Luckily, the game has a hidden easy mode, making any fight a breeze. Enter the Nail Gun.
You might think it's just a situational skill, considering it's limited ammo, but once built around, it'll allow you to channel your inner Space Marine and steamroll any fight.

It works kinda like this:

First off, let's talk about some Nail Gun advantages:

• You can keep your distance from enemies - less risk of taking damage.
  
• Repeated shots will stunlock enemies - stopping them from closing on you and attacking.
  
• Massively speeds up combat, since the enemies can't block or dodge the shots (aside from shielded soldiers - this is where bombs come in), so you can just keep dealing damage rather than constantly defending and trying to get attacks in.

As for disadvantages:

• Limited ammo requires some basic resource management.
  
• Turns game into a faceroll from late Chapter 1 onwards. This playstyle maximizes speed and efficiency. Might not be ideal for fans of SL1 Dark Souls runs.

Alright, so how we go about building out Roy to maximize the Nailer's potential?

First off, by getting enough ammo.
It can get really costly really quick, which is why we want to get the Good reputation - and the feat 'Charismatic' - as soon as possible, as it'll allow us to buy ammo 50% cheaper.
That means never finishing off enemies, choosing the nice guy quest solutions and answers as much as possible, sparing enemies whenever prompted to choose their fate and so on.

I don't know every single choice going into the good rep, but from what I've heard you can get it before finishing Chapter 1. Personally, I didn't get it till Chapter 3, but still managed to get by, with some smart Serum management.

Managing your Serum
Once you get Charismatic, Serum isn't a problem, but before that, you'll have to keep a few things in mind:

• Never buy melee weapons or armors from vendors. You can find every single one throughout the game, so long as you check the chests.
  
• Sell any expensive components you don't need for upgrades - this includes Bones, Alloys, Chemical and Electrical Components. Try to keep some chemicals (~5 is usually enough) on hand though, in case you need to craft bombs for dealing with large groups or shielded soldiers.
  
• Sell weapons and armors you're not using.
  
• Don't craft Health Injections, unless you're in a pinch during combat. It's cheaper to buy them from vendors.
  
• Before you get Charismatic, buy as much Hardware as you can from vendors and craft the ammunition yourself. Once you reach good reputation, buy ammo directly instead. From Chapter 2 onwards, it's a good idea to stock up about 100 ammo before going on quests

Following these few rules, you should always have enough ammo to deal with any encounter. Now, onto the build itself.

When it comes to building up Roy, you'll have some leeway, as aside from a few important ones, most skills can be treated as fillers.

Quick Learner, Combat Spirit, Combat Genius
You should invest in these first. More XP = more levels, more skills, more power

Snooper, Searcher
Next priority after XP feats. These give you more loot from defeated enemies, including valuable materials you can sell, so you can always have enough ammunition for the Nailer.

Apprentice Handiwork, Expert Handiwork
These unlock extra upgrades for melee weapons and armor. You'll want to stay at a distance as much as possible, so these are not very high priority.

Charismatic
50% reducion in vendor prices. You get it for free once you reach good reputation. The sooner the better.

Natural Leader
50% extra HP & damage for comapanions, free once you reach excellent reputation. Nice to have, but you'll do just fine without it, so don't worry if you never get the required rep.

We'll want to go into Renegade and Combat to make the most out of this playstyle. I'll list the highly recommended skills below. Aside from that, you can pick whatever you want. If you also want to get the Specialist achievement, I recommend maxing out Combat over Renegade, as it'll help you with survivability.
I'll mark the recommended skill levels with *

Renegade
First Aid - *
Allows you to use health injections while moving, pretty much mandatory.

Hotshot - ***
Lowers the cost of crafting ammunition and greatly inproves Nail Gun damage. Pretty much a cornerstone of this playstyle.

Subtility - **
5% chance to wound enemies on melee attacks and 15% on Nailer attacks. Great debuff, as wounded enemies walk and attack much slower, letting you focus on shooting off their faces, rather than dodging.

Deadly Shadow, Feather Foot, Assassin - * to ***
Stealth can be useful, especially early on - allowing you to take out some enemies before staring the encounter. You can level them up if you want, though I mostly consider them fillers for getting the previous two skills.

Combat:
Science of Evasion - ***
Massive damage reducion while dodging and faster recovery afterwards. Best defensive skill in the game, if you ask me.

Combat Trance - ***
Slows down time. It's pretty meh for melee combat, as enemies will still dodge and block at the same rate. Godlike for Nail Gun, allowing you riddle them with bullets before they get anywhere near you. Talk about bullet time!

Offensive Roll * to ***
1 point gives you extra dodge distance, which is great. 2 or 3 give you extra crit chance on melee attacks after dodging, which is nice for dealing with shielded troopers early on. Once you get Charismatic, you can cheaply stock up on bombs, so you can just use these to knock them down and turn them into swiss cheese.

That's about it for the most useful skills, aside from these feel free to grab whatever you want. Once again, if you're going for Specialist achievement, I suggest you max out Combat tree.

As far as progression goes, I'd suggest this order:

• First Aid *
  
• Science of Evasion ***
  
• Renegade fillers to unlock Hotshot
  
• Hotshot ***
  
• Combat fillers to unlock Combat Trance
  
• Combat Trance ***
  
• Subtility **
  
• Whatever you want

Early on combat can be quite difficult, especially since you won't have access to Nail Gun from the start. Focus on dodging and getting melee attacks in when you can, use bombs and traps when fighting bigger groups. Once you get the 3 quests to prepare for the escape, return to the mole tunnels first to pick up the gun.

Whenever you're in a fight with multiple ranged opponents, try to deal with them first, unless they're focusing on your companion. You can easily keep melee enemies at a distance with Nailer's stunlock, but you'll still be a sitting duck if you don't deal with rifle users first.

For the companions - use either defensive stance, so they can keep aggro off you for longer before going down, or have them focus on ranged enemies.

As you progress through the game, it'll keep getting easier and easier.

Here are some more examples of how it works in practice:

That's about it, thanks for reading. Now go and turn some Aurora goons to swiss cheese!