Layers
Unity has a layer system and a sprite sorting system. The game makes extensive use of these systems and the configuration may be useful to modders. This page will describe each layer and what its used for.
Object layers
Here is an article explaining Unity's object layers.
0: Default
Comes with Unity. Not used for anything.
1: TransparentFX
Comes with Unity. Not used for anything.
2: Ignore Raycast
Comes with Unity. Not used for anything.
4: Water
The water layer. Liquid body (water and lava) colliders are on this layer. Used by firearms to create splash effects. Why is it called "Water" if there's also lava? Because there wasn't always lava.
5: UI
The UI is on this layer.
8: Post Processing
Post processing volumes are on this layers.
9: Objects
Most physical objects are on this layer. Objects on this layer collide with each other, the room, and some debris. If you want to create an object that colliders with other objects, this is the layer to put it on.
10: Debris
Most debris is on this layer. Debris only colliders with the walls, ceiling, and floor.
11: Bounds
Collides with everything. The chamber walls are on this layer.
12: Overlay
Not used for anything.
13: CollidingDebris
Colliding debris colliders with the room and objects.
14: Portal
Not used for anything.
15: LightSprite
Objects on this layer are rendered by the lighting camera. Most objects in this layer are large radial gradients.
16: ScreenUI
Objects on this layer are rendered under the normal UI and above game objects. They are not affected by post processing effects.
17: Energy
Energy weapons that should collide with each other, but not anything else, are on this layer.
18: HoverSurface
Unused.
19: ImmobilityField
Immobility capture fields have a collider on this layer. Other objects can cheaply query this layer to find out if they are inside an immobility capture field.
31: Thumbnail
When a contraption is saved, the whole thing is taken to a thumbnail room where everything is on this layer.
Sorting layers
Here is an article explaining Unity's sorting layers.
Bottom
The lowest sorting layer. Used by map decorations and such.
Background
Originally created for the background limbs of humans. It's used by objects that have parts that necessarily need to be behind most other objects.
Default
Most objects are on this layer.
Portals
Unused.
Foreground
Originally created for the foreground limbs of humans. It's used by objects that have parts that necessarily need to be in front of most other objects.
Bubbles
Used by some effects and renderers that should not render outside of water bodies.
Top
The top sorting layer. Not actually the top though. Contains map decorations like water and such.
Decals
Contains decals that are supposed to be shown on top of everything. Does not mean all decals are on this layer. Rarely used.