Prototype Transhuman seems like it can't be an option for this character, as it's a birth status thing, and supplements won't be available until after play.
If you want a weapon for silent take downs, my recommendation is a double-edged sword. The dart pistol. Narcoject can often take a target out in one quick, easy shot. However, it's an exotic weapon proficiency, and somewhat limited in application. Turns out, stick n shock works on drones and sometimes even spirits, but narcoject? Not so much.
Melee combat, though, is hard to do as damage values tend to be keyed off of strength, and are rather low unless you have a strength score of 'yes' or a dice pool of 'all of them.' For that, I would generally recommend things with fixed damage unless you can get at least six strength. Shock gloves, stun baton, the ever deadly monofilament whip. Actually, a monofilament whip adept can be terrifying with relatively little investment. Goes great in a fingertip compartment. You can even make it a weapon focus, if your GM will let you get away with it.
As for augmentation on an adept? There are many augmentations that can be worth it. Spend that essence carefully, but don't think you have to have essence 6, magic 6 to be effective. It's a trade-off, but it's one you can come out ahead on. For example, if you want to hit your augmented maximum on agility (four greater than your base stat), doing that directly through power points would cost you four power points, one per point of agility. Rating 4 muscle toner would cost .8 essence, losing you one point of magic and the corresponding power point. (Note: You can't start the game with muscle toner 4, but muscle toner 2 may be a good investment for your character.) This tends to be a much more attractive deal for adepts than mages, as you rarely roll your magic stat for anything, save a select few powers you don't have to take.
In combat, do note that perhaps the single most important number on your character sheet is initiative. The Improved Reflexes is probably the most important, and eventually you'll probably want that at rating 3, though not necessarily at character creation. There are some other options for getting it up (Cram and Jazz spring to mind), if you can't fit it in right off the bat, though.
