Runes
There is a Rune inside of a whale carcass along the wharf. It’s not too far from where you start the mission.
Buy a Rune from the black market in town.
The Overseer building in the canal area has a Rune on a table where someone is speaking to the crowd. Steal that after defeating the Overseers, or Blink/Far Reach to steal it from the table.
Get into the canal near the Overseer building. Look for a gate where the water comes into the canal and use your Crossbow to break a wooden plank that’s partially blocking the flow. This causes a Rune to slide down toward you.
Unlock a safe in the Overseer building, on the third floor. It has 225 coins and a Rune inside of it. The Combination is (516).
A small path stretches to the right before you get to the canal area. This leads to a two-floor apartment building. Kill the two Overseers that are exploring the place, and look for the Outsider Shrine on the second floor.
Bonecharms
The infested building has a Bonecharm on the second floor. It’s inside of a nest, and is visible once you destroy the Nest and kill the Bloodflies around it.
Outside of the Overseer building is a table with a Rune and a Bonecharm. Kill the Overseers to loot these items, or Blink/Far Reach onto the table and carefully steal the goodies before the crowd freaks out and alerts the Overseers to your presence.
Blink/Far Reach across the rooftops from the Overseer building. Two structures to the side there is a roof with a corpse on it. Kill the Bloodflies that are growing, and take a Bonecharm from the dead person.
An apartment is down a side path before you reach the canal area. Kill two Overseers inside of it, and get a Bonecharm off of the floor, on the second story of the building.
Go to the Winslow Safe Company by the end of the level. On the main floor is a massive safe. Put (508) into the lock to open it and get a Bonecharm.
Near the top of the Overseer building you find a locked Interrogation Room. Get the Key from an Overseer in the next room to the right, and unlock the door. Inside is a Corrupt Bonecharm.
Paintings
Before you get into the canal area, there is a side road that leads to a single apartment building. Look in here and defeat two Overseers that are searching the apartment for contraband. A Painting of the Outsider is on the second floor.
The third floor of the Overseer building has a Painting on the wall. It’s near a safe that has a Rune locked inside of it.
Hypatia’s apartment has a Painting in the main hallway. She lives above the Winslow Safe Company, in the latter part of the mission.
For the last painting, locate a small apartment near the beginning of the mission area. To reach it, Blink or Far Reach up to a balcony with a large sign above it. Enter the apartment and search to collect this painting.
Blueprints
Fire Hardening Treatment has a Blueprint inside the Overseer’s building. It’s up a couple of floors, in an important Overseer’s office. Look on the desk for it.
For the second blueprint, there is a safe with a blurprint inside in an apartment overlooking the docks. It's not far from the dead whale, so get this when you grab the Rune inside the dead whale. Use Blink or Far Reach to enter the apartment above the docks.