Hadn't seen anyone mention this so I thought I would.

The description of the cell:

You are in an iron chamber, the walls are lined with iron pipes. 
There are chains suspended from the pipes and rusted gears are scattered about the floor. 
The sound of dripping water echoes in the chamber.

Sounds like the description given in QR code #9:

You are in a rusted iron chamber. Water is trickling from large iron pipes above you. 
On the wall someone has scrawled:
“When in your house black crows give birth to white doves, then you will be called wise".

Which fits with the skeleton/map/knife/note piece.  Guy wrote the message on the wall before he died.  I tried look at wall and a few other combinations of words and got nothing.  Tried typing key words of the phrase into the keypad and nothing.  Maybe the message maps to the clusters on the map somehow.