Matting

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Matting
Create Matte
Creates a matte, either to one or to multiple layers (Win: Ctrl+Alt+Z, Win [German]: Shift+Z, Mac: macControl+Z).
Quick Track Matte created to a Layer
With one layer selected, this function will create an empty track matte layer to the selected layer. By default, it will be two times the size of the current composition. This is to have extra pixels for when the matte will be parented or animated, so it doesn't get cut off on the edges when moving. If you open up the Settings and go to the Matting tab, you can set another default size for the matte layer.
If the selected layer already has a track matte, Workflower will execute Merge Mattes (see below), so that both mattes will be matted to the selected layer.
By default, mattes are created with Collapse Transformation enabled. In the Matting Settings, you can also disable this option.
Multi-Layer Matte
Matte applied to three Layers at once
With several layers selected, this function will create a Multi-Layer Matte that applies to all selected layers. You have the option of either using a custom matte layer or an already existing layer from the comp.
Group Matte
Creating a Group Matte
A Group Matte applied to every Group Layer
With a group header selected, Workflower will create a Group Matte. By default, the Group Matte is a custom layer, added to the top of the group. Merge Mattes will be executed on every layer, contained in the group, to apply the Group Matte. You can also choose another layer from the comp as your matte layer. Simply choose the desired layer the dropdown on the Group Matte Settings effect and hit Refresh Connections.
Group Matte Effect
If you have sub-groups with Group Mattes themselves, Workflower will apply the Group Matte of the sub-group as well as the Group Matte of the higher group to every layer. 
By default, Group Mattes won't be applied to disabled layers. You can choose to apply them too by going to the Matting Settings and deactivating that setting.
To disable a Group Matte temporarily, just deactivate the effect switch of the Group Matte effect.
Removing a Group Matte
To remove a Group Matte, simply select the group header and hit Create Matte again. All Group Mattes will be removed from the layers. If the layers only had one track matte aside from the Group Matte, the Matte Merge will be undone and the matte converted back to a single track matte.
Please only remove the Group Matte as described above. Do not simply delete the Group Matte layer. If you would then execute Refresh Layout, the Group Matte will be removed - however, Matte Merge layers will remain above the group layers, even if they have no matting effect left on them. (Tip: If you quickly want to delete empty Matte Merge layers, select them and execute Delete Layer / Clone / Group. This will remove the matte layers as well as the track matte state of the layer below.)
Order of Group Mattes, Group Clones, and Group Linked Adjustment Layers
Group Mattes, Group Clones, and Group Linked Adjustment Layers have a specific layer order when used in conjunction. Read up here for more information.
Merge Mattes
Merges multiple mattes into one track matte layer to a layer (Win: Ctrl+Alt+Shift+Z, Mac: no default shortcut).
Creating the Matte Merge Layer
Left: Base and Matte Layers selected before Matte Merge; Right: The created Matte Merge Layer and Matte Collection Group
First, select the layer you want the mattes to be matted to. If the layer already has a track matte, you can also select the track matte. After that, select your desired matte layers and hit Merge Mattes. A Matte Merge Layer will be created and used as a track matte for the layer that the mattes should be matted to. On the Matte Merge Layer, matting effects, using AE's Calculations effect, for each matte layer will have been created. If the matte layers are directly above the base layer and are disabled, they will be put into a Matte Collection Group. (For more information on this, see below.)
If the matte layers have Collapse Transformation enabled, or have comp dimensions and are unmoved, the matte effects on the Matte Merge Layer will reference those layers directly. For all other matte layers, a Precomp Clone of the layer will be created in order to fit it to comp dimensions.
As of now, when changing the comp size, Matte Merge layers will not be adjusted to the new size automatically. To make the Matte Merge layer work again, you need to go to its Solid Settings and hit Make Comp Size. It is recommended to disable Affect all layers that use this solid. (Only when you are sure that no Workflower layer other than the Matte Merge layers of the comp with a new size use this solid, you may enable Affect all layers that use this solid.) (As of version 1.0.4, Matte Merge layers resize automatically if the comp size has been changed.)
Modifying Mattes
Multiple Matting Effects
On the Matte Merge Layer, you can use the Calculations effects to modify your mattes by changing the blending modes (either to Normal, Stencil Alpha, Stencil Luma, Silhouette Alpha, or Silhouette Luma), the opacity, the inverted state, and the matte order by moving the Calculations effects around.
Modifying Matte Source Layers
Matte Layer Settings Effect
To all matte source layers, a Matte Layer Settings effect will be applied. Using the effect, you can choose whether in/out points should be respected and modify the blending mode, inverted state, and opacity. Modifying these states on the layer itself - as compared to modifying it on the Matte Merge Layer effect - is useful when having a matte that is applied to multiple layers so that changes don't have to be made on each Matte Merge Layer individually.
Invisible Mattes
On the Matte Layer Settings effect, you also have the option to enable Invisible Matte. That means that the layer will be set to 0% opacity while it is still enabled. That way, the layer will behave like a regular track matte: It is not visible but you can move it with your cursor around in the composition viewer (which would not be possible with a disabled layer).
You can also very quickly show the layer itself again by clicking on Show Matte. This will temporarily set the opacity back to its actual value.
On Invisible Mattes, you can't set the Opacity on the Matte Layer Settings effect to From this Layer (since it will be at 0% opacity). You can only set it to either Custom Opacity or From Matte Merge Layer Effect.
Layers that are put into a Matte Collection Group will be set to Invisible Matte. Other matte source layers won't be set to Invisible Matte by default, however.
Adding new Mattes
To add new mattes to an already existing Matte Merge Layer, simply select the Matte Merge Layer first (or its matted layer), then the new matte layers, and hit Merge Mattes again. You can also add new mattes using Add / Remove Layer References. (Be aware, though, that, using this function, the order of selection is reversed.)
If you select either the matted layer or the Matte Merge Layer and execute Create Matte, an empty matte will be created to the Matte Merge.
Updating Effect Names & Clones
If you have no layer selected and you execute Merge Mattes, all matting effects on the Matte Merge Layer will be renamed to the current name of the referenced layer. Perform this action after having changed layer names and then working on the Matte Merge Layer since it is difficult to read the layer name from the layer control on the matting effect.
When executing Merge Mattes with no layer selected, all unused matte clones will be deleted, too. 
Matte Collection Groups
A Matte Collection Group above the Matte Merge Layer
Creating a Matte Collection Group
If the selected matte layers are directly above the layer that they should be matted to AND they are disabled, a Matte Collection Group will be created above the Matte Merge Layer, into which the matte layers will be put. The Matte Collection Group always needs to stay directly above the Matte Merge Layer if new mattes should be put into it as well. If new mattes are added to the Matte Merge Layer and the Matte Collection Group is not directly above, they won't be automatically added. (However, you can of course still put them into the group yourself.)
All layers that are put into the Matte Collection Group will be turned into an Invisible Matte. Read up more about Invisible Mattes here. (On the other hand, layers that are not put into a Matte Collection Group, won't be turned into Invisible Mattes.)
You can disable the creation of Matte Collection Groups too by going to the Matting Settings.
Properties of Matte Collection Groups
A Matte Collection Group differs from a normal group insofar that it inherits the label color from its containing group, as well as its parent if the containing group is a parented group.
If Precomp Clones are created for a Matte Merge, they will be put into a custom Matte Clone Collection Group.
Matte Collection Groups are symbolized by the Icon ∆, Matte Clone Collection Groups by ∆∆.
Converting Matte Collection Groups
You can convert a regular group to a Matte Collection Group by selecting it and hitting Merge Mattes. If you select a Matte Collection Group and hit Merge Mattes, it will convert it to a Matte Clone Collection Group - but only if it doesn't already exist - otherwise, it will just convert it back to a regular group. If you select a Matte Clone Collection Group and hit Merge Mattes, it will convert it to a regular group.