How do I remain undetected for the "Cloak and Daggers" mission?
You can be detected by these people and still get the reward for being sneaky. As long as they don't go Hostile, you're fine.
You can make this jump without the leg aug, but you need the Punch Through Walls aug to go this way. This also involves snapping a guy's neck and will ruin a pacifist playthrough. Also throwing a grenade at the wall works, and only knocks the guy unconscious., or you could just use the ventilation ducts attached to the wall...
As before, if they don't go Hostile, you are fine.
The game will tell you if you fail the sneaky objective.
Once you cross from the Detroit Downtown map into the Derelict Row map (either go through the sewers or enter the Derelict Row complex) you can't get your alert status to "hostile". It is ok to get "alarmed". In the Detroit streets outside, you can fight your way in if you like, it will not count against you.
The main street entrance has a path on the left you can use to sneak to the sewer entrance.
The easiest way to the cache is to sneak in through the sewers to the end (OK to get hostile in the sewers), then go up the other ladder past the guards in the sewer. Once up, there are a few barrels by the wall. Move them aside and go through the hole. You will have just found the stash. Return to your contact and you will get the bonus.
Edit: I forgot to point out that you don't need any augments to sneak in through the sewers.
If you want to be really meta-sneaky, it's entirely valid to take out everyone in the area before accepting the mission. Guards can't detect you if they're already unconscious :)