When you get back to the first area, four more guards will have arrived. Avoid them by walking across the planks back to the Abbey building, and grab the bottle of chloroform from the scaffolding here. Go to the roof overlooking the new gang, and shoot a crossbow bolt in the ground right between them. As they all rush to look, throw the bottle, then drag them all to a nearby doorway for safekeeping. Revisit the shopkeeper and hand over the prototype in return for a pretty generous payment and a Special Action.
Scoop up your ingots and blueprint (Blueprint 3/3) and then purchase what you need. Go ahead and splurge a bit because 1) you just got a discount, and 2), you're about to rob the place.
If you snagged all the Blueprints, you'll have the choice for new Masterwork upgrades. Playstyles vary, but for Ghost/Clean Hands I recommend the multiple targeting cross bow and the anti-hound howlers. The former can actually be used on hounds, which dont' count as kills, and the latter can be handy in the final fight. You will face a lot of witches too, but it's better to pick them off from their orderly patrol routes than to send them screaming willy nilly all over the map.
Once you're fully kitted out, fall back a bit to peer into the barred window nearish the main entrance. You'll see a chain with one of those red casings, like the kind we used to kibosh the elevator back in dear old Addermire. Repeat tactics by shooting this one out with a crossbow bolt.
Turn around. If you look around the floor by the part of room opposite the shopkeeper, you'll see a valve wheel like the one we used to fix the water leak aboard the Wale (this shop is just full of so many memories).
Pick it up and take it with you, down to the docks, and past that one ship that doesn't belong to you, to the grate blocking the canal. The wheel practically leaps out of your hands once you get close to the gate control- just give in a spin to open the grate, then enter and find a chain you can climb up (there's even a helpful black market sigil on the wall, in case you had doubts. Climb up, choke out yet another peaceful entrepreneur, and fill your pockets with gear, gold, and that final Rune (Rune 6/6). Also the safe combination, because that's where we're headed next.
If you left any hives intact during your first visit, grab the rum from the stairs here and return to apartment where you dealt with the nest keeper. Clear out any threatening hives (again being careful not to torch the nest keeper), then open the safe with the combination from the blackmarket. There's also a small upper level here with decent loot.
That's the last of the major acquisitions in Cyria Gardens. There is a moderate stash by the guards on the watchtower side of Conservatory, and of course the guards themselves carry a bit of coin.
Remember that there are a fair number of sleep darts inside the Conservatory itself, if you need them. You might also grab the few items above the Wall of Light, accessible from an open window on the Conservatory side.
Either way, once your avarice is sated you can head back to Meagan for extraction.