Intake, exhaust, programmer, custom tune.
Being a 2015 for the programmer and custom tune you'll need an unlocked PCM. You can either trade yours, buy one or send yours in to be unlocked.
I'd talk with Matt at Moe's Performance about your options. He can hook you up with a complete tuning package.
Muffler is up to you. Since you have a MDS equipped motor, I'd do a muffler swap and leave the rear resonator(s) on the truck to reduce drone. Or you can go full catback. What is your current exhaust configuration?
As far as the intake, some would say your stock one flows just fine. I tend to agree except for one aspect of the CAI that really helps and that is improved throttle response.
Put all those mods together as they work best as a system. In my view, I'd do intake and exhaust, then the programming.