Cloning

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Cloning
Clone and Precomp
Clones layers using linked expressions and precomps the cloned layers (Win: Ctrl+Alt+Shift+W, Mac: macControl+W).
Precomp Clone Effect
You can make use of a Precomp Clone when you, for example, need to merge layers into one layer to add effects directly to the precomp, or to have the precomp layer fit to comp size to be able to reference it by another layer's effect. The advantage of using Clone and Precomp instead of simply precomping is that you keep all layers within your main comp. That way, you can still work with all layers in your main comp, set parents within that comp, and reference layers in effects without the confusion of working within several comps. Also, it's much easier to see the whole project structure if you mostly work in one comp.
Parented layers and layers, referenced by effects, will be cloned and precomped as well. If enabled, the active camera, as well as lights, will be cloned, too.
Make sure that all contained source layers, as well as your current comp, have unique names. Otherwise, the expressions on the clone layers cannot reference the correct source layers.
Refreshing Layer Attributes
All linkable attributes are linked by expressions within the clone comp. Besides all transform and effects properties, you can disable/enable layers and effects themselves too and they will be live-disabled/enabled in the clone comp.
If you change non-linkable attributes (like adding an effect/mask, changing layer/effects/masks order, set another blending mode, etc.), you need to use Refresh Connections or Quick Refresh Connections (or the even simpler and faster Quick Refresh Clone Connections within Refresh Layout) afterward to update the corresponding clone layer.
If you encounter a bug with either Refresh Connections or Quick Refresh Connections, you might want to try the other function instead as it will often solve the issue.
Sometimes it may happen that expression errors come up directly after creating a Precomp Clone or when refreshing a Precomp Clone. Check out the Expression Errors section of Known Bugs for more information.
Duplicating a Precomp Clone
Dependent Clones, as indicated by the ｄ Icon that were duplicated from 'BUILDING 3D || Group Clone'
When you duplicate a Precomp Clone and hit Refresh Connections, a unique clone comp will be created for the duplicated clone, so that there will be two Precomp Clones then. If you simply want to reference the original clone comp, you need to delete the Settings effect as well as the Cloned Layer effects on the duplicated Precomp Clone to make it dependent on the original clone comp. 
As of version 1.1, you can also just select the Precomp Clone layer and execute Duplicate Group. This will duplicate the Precomp Clone and remove the Settings and Cloned Layer effects to make it a Dependent Clone.
Adding / Removing Clone Layers
Add/Remove Layers by Duplicating/Removing the Cloned Layer Effect
You can add new clone layers to the Precomp Clone by duplicating a Cloned Layer effect on the Precomp Clone layer, and then selecting a new layer by using the layer dropdown. You can remove a clone layer by deleting its Cloned Layer effect.
There's the option of using the Add / Remove Layer References function as well to add or remove clone layers which generally is a bit faster than selecting layers via the dropdown.
Unlink Properties
An Unlinked Precomp Clone, as indicated by the  ：Ｕ  ： Icon
By default, all clone layer properties are linked to their corresponding source layer properties. You can also, however, unlink all properties by unchecking Link Properties via Expressions. Expressions generally use up quite some computing power and if you work with a lot of Precomp Clones, this can significantly slow down your comp. That's why it might be useful to unlink properties after you're done working with your clone layers. When you get back to working on the clone, you can link properties again.
You can also use Link / Unlink Properties to link/unlink in a quicker way than (un)checking the checkbox. You can also link/unlink all properties within the whole comp or project at once using Link / Unlink Properties.
Prime Clone
Prime Clone with its contained Source Layers set to 0% Opacity
A Prime Clone differs from a regular Precomp Clone insofar that the opacity of all contained source layers will be set to 0% while their corresponding clone layers in the clone comp retain their normal opacity and the Prime Clone precomp layer itself is the only layer left visible in the main comp. Basically, a Prime Clone is like a regular precomp, yet you don't lose all layers within the main comp, and you can manipulate the precomp layer while still being able to work on the contained layers - add effects, masks, change transforms, etc. - and see the result live on the precomp layer.
Opacity of Prime Clone Source Layers
Prime Clone Source Layer Opacity Slider
Because the opacity of all contained layers is set to 0%, AE's opacity slider is not usable anymore. That's why Workflower will add an effect to the layer with a custom opacity slider. Use this one to modify the layer's opacity. Since hitting T won't work anymore to reveal the opacity slider in the timeline, you can also execute Reveal Layer Opacity by using a shortcut to reveal Workflower's opacity slider.
Working on Prime Clone Source Layers
Prime Clone showing its Layers, as indicated by the » Icon Marker
Because the only layer visible is the Prime Clone precomp layer, not its source layers, you can see changes instantly when you change properties linked by expressions.
However, when you, for example, add effects or change the layer order, you always need to execute Refresh Connections. (Most of the time, just executing Refresh Layout and its built-in Quick Refresh Clone Connections should work, too.) Refreshing can be useful when making minor changes, however, when you have to work quite a lot on the Prime Clone layers, you can also show the source layers themselves by either clicking on Show Layers on the Precomp Clone effect (and then executing Refresh Layout) or just hitting Show Clone Layers. The Prime Clone precomp layer will then become invisible and the opacity of all source layers will be set to their actual value.
Working with clone layers shown is computationally faster since the properties don't have to processed through expressions. When you're done working on your layers, hit Show Clone Layers again to hide them and show the Prime Clone precomp layer again.
Soloing Prime Clone Source Layers
You can solo Prime Clone source layers and they will be live-soloed in the clone comp. (This won't work on regular Precomp Clones.) However, be aware that the Prime Clone layer needs to be soloed as well for this to work. Instead of always having to solo the Prime Clone layer as well, you can just solo your desired source layers, hit Refresh Layout and if they are contained in a Prime Clone, the Prime Clone layer will be soloed automatically. If only the Prime Clone layer and no contained layers are soloed, all clone layers will be visible.
Stacking Prime Clones
Prime Clones stacked on Top of each other
Prime Clone source layers are symbolized by the Icon • and they indent further depending on their Prime Clone depth level. That way you can create Prime Clones of Prime Clones and keep merging layers into precomps, while retaining a clear visual representation of the layer/precomp structure.
Group Clone
A Group Clone, as indicated by the  [ｇ]  Icon, containing another Group Clone
You can create a Group Clone by selecting the group header and then executing Clone and Precomp. A Group Clone differs from a normal Precomp Clone insofar that, when executing Refresh Connections, group layers will be automatically added/removed to/from the Group Clone if they have been added/removed to/from the group.
Only layers below the Group Clone layer will be added to the clone comp. That allows you, for example, to add a track matte or other manipulations onto the Group Clone without these layers being added to the clone. The only exception to this is when the Group Clone is a track matte to another layer. In that case, the layer below the Group Clone won't be added to the clone comp.
You can create Group Clones of groups within another Group Clone too. Only the Group Clone itself (not its contained layers) will be then added to the higher Group Clone.
Because of its nature, you cannot add/remove layers to/from the Group Clone itself or use a Custom Layer Order.
Order of Group Clones, Group Mattes, and Group Linked Adjustment Layers
Group Clones, Group Mattes, and Group Linked Adjustment Layers have a specific layer order when used in conjunction. Read up here for more information.
Custom Layer Order
Precomp Clone Layers with a Custom Order
By default, the layer order within a Precomp Clone is the same as it is in the main comp. However, when you, for example, want to make use of a Precomp Clone to create a track matte layer, you might want to change the layer order to customize your matte. On the Precomp Clone effect, switch the Layer Order to Custom Order and move the Cloned Layer effects to the position you want them to be in. Then execute Refresh Connections and the custom layer order will be created within the Precomp Clone.
Custom Precomp Size
Precomp Clone with a Custom Size
A Precomp Clone is created with comp size by default. But you can apply a custom size to it too. You can customize the width and height, as well as whether the area should be shifted on the X- and Y-axis. Select the desired values and hit Refresh Connections. The size will be cropped/expanded to the defined area and the position of the Precomp Clone layer will be corrected in order to stay at exactly the same position (even when the position is animated).
If you want to see a visual preview of how the new size of the Precomp Clone is going to look like before applying it, execute Preview Custom Clone Size.
As of now, a custom precomp size only works if its contained layers are 2D.
Enabling Precomp Transforms
A Prime Group Clone with Enabled Transforms in order to have Tracking Data applied to it
By default, transforms of a Precomp Clone are locked. You can, however, also enable transforms. If it's a Prime Clone, its contained layers in the main comp will be parented to the Prime Clone (if their existing parent is not to another layer in the clone), so that when you move the Prime Clone, all layers will move accordingly. The clone layers within the clone comp, however, will not be parented. If it's a regular Precomp Clone, its contained layers won't be affected. If the Prime Clone contains other Precomp Clones without enabled transforms, their transforms will be enabled.
As of now, enabled precomp transforms when you're using a Prime Clone only work with 2D layers. If you want to use 3D layers, its z-position must be at 0 for the precomp transforms to properly work.
Custom Clone Layer States
Cloned Layer Effect
You can set custom states for all clone layers individually:
Enabled/Disabled: You can enable a clone layer when it's disabled within the main comp and vice versa. Enable the clone layer and disable the source layer when you, for example, want to build a track matte layer using the Precomp Clone and the contained layers must not appear in the comp itself.
Opacity: You can set a custom opacity.
Trim In/Out Point like Source: When enabled, the clone layer will get in/out points of the source layer. When disabled, it will stretch across the entire comp.
Blending Mode: You can set the blending mode to several options:
Like Source
Normal
Stencil Alpha
Stencil Luma
Silhouette Alpha
Silhouette Luma
Change the blending mode when making use of a Precomp Clone to create a matte layer. You can set the layers to either Stencil or Silhouette to build your custom matte.
Track Matte: Changing the track matte state might be useful when layers within the main comp have a track matte and you want the clone layer without a track matte. Or vice versa: set a track matte state for a clone layer when you want to build a custom matte within the clone comp.
3D Precomp Clones [Experimental]
3D Precomp Clone with the Z-Position of its contained Layers stuck to 0.
3D Precomp Clones are only an experimental features. That's why they are disabled by default. To use them, go to Settings, then to the Cloning tab, and enable Use 3D Precomp Clones. As of now, there are several limitations when using 3D Clones:
Regular Refresh Connections doesn't work with 3D Prime Clones. If you execute it, Quick Refresh Connections will be executed instead.
Unlinking 3D Prime Clones won't work. When you turn it off, they will be linked again.
​New Clone Sizes cannot be applied to 3D Prime Clones. You can only use comp size.
3D Prime Clones are incompatible with contained Matte Merges. Transforms of matte layers won't match actual transforms. Use Precomp Clones to create track mattes with multiple matte layers instead.
Other bugs might occur when using 3D Precomp Clones.
You can activate 3D Precomp Clones by clicking AE's 3D switch and then executing Refresh Connections. (This only works when Precomp Transforms are enabled. Otherwise, the Precomp Clone will be set back to 2D.) 
If Collapse Transformation is disabled on a Prime Clone, all contained layers will be converted to 3D but stuck to the z-position of the Precomp Clone layer. That way you basically create a 2D comp within the clone comp itself that then is turned 3D in the main comp. The difference to just creating a simple precomp, however, is that you can see all your contained 2D layers in 3D space and position them, apply effects, etc. in the context of the main 3D comp.
The Orientation property of the contained layers will be set to [0, 0, 0] by expression to stick them to the Precomp Clone layer. Make sure to use Rotation instead of Orientation to rotate the layers.
Also, an expression is applied to the Anchor Point as well to set its z-value to 0. That means, however, that cannot apply an expression yourself to the Anchor Point.
If Collapse Transformation is enabled on a Prime Clone, the contained layers will also be converted to 3D, however, they won't be stuck to the z-position of the Precomp Clone layer and can be moved around freely.
The behavior of 3D Precomp Clones, described above, only applies to Prime Clones. If the clone is a regular clone, the contained layers won't be affected by the clone's 3D state.
Clone and Precomp Modes
Clone and Precomp Mode Dropdown
There are two different Clone & Precomp modes. By default, a mix between the two modes will be executed. You can choose to only execute one of them, too. Go to Settings / Cloning / Clone and Precomp Mode to change the mode.
Faster for fewer Properties: This mode will copy all layers to the clone comp and go into every property to link them to the source layer.
Advantages:
It is faster for fewer properties (~ < 100 effects & layers).
The user's clipboard will stay intact.
It will not cause problems with AE's Undo/Redo.
Disadvantages:
It can get quite slow when dealing with a lot of layers and effects.
If you have another script installed that uses a callback function to display errors that happen within the application, the mode can cause various errors. Go to Known Bugs for more information.
Faster for more Properties: This mode will use AE's native function Copy with Property Links to copy all layers to the clone comp.
Advantages:
It is faster for more properties (~ > 100 effects & layers).
Disadvantages:
Since the mode uses AE's native function, the user's clipboard will get overwritten in order to contain the layers copied to the clone comp.
If you undo the cloning action and then try to redo it after that, you will not be able to recreate the original state but rather a state midway through the function's execution. See Known Bugs for more information.
Clone in Comp
Clones a layer in comp using a Calculations or Set Matte effect (Win: Shift+N, Mac: no default shortcut).
Note for Mac users and when using Individual Scripts Mode on Windows:
The default shortcut for this function has been removed in version 1.1. (If you still want to use a shortcut, please set it yourself in the shortcuts panel.)
Clone in Comp of '3D Building' used to split the Layer
Advantages of a Clone in Comp
A Clone in Comp has a major advantage compared to a Precomp Clone:
Because the image data is not linked by expressions but by an effect, you don't have to hit Refresh Connections nearly as often as you would when using a Precomp Clone. The Clone in Comp updates automatically every time you add/remove effects/masks, change the order of effects/masks, or modify non-linkable effect/mask parameters. However, changes on layer switches, parents, blending modes, and layer time properties still require refreshing. For more on refreshing Clone in Comp connections, see its chapter.
You can use a Clone in Comp for several purposes (only examples):
As a track matte: A track matte layer always needs to be on top of the matted layer. Sometimes, this is what you want but other times you just want to use an existing layer from the comp that's at a totally different layer index, that you don't want to change. You could use a regular Set Matte effect to achieve this matte. However, for this to work, all transform properties need to be the same or both layers need Collapse Transformation enabled. That's not always the case, and this is what a Clone in Comp can be useful for: It creates an active clone of the layer to be able to place it directly above the other layer and use it as a track matte so that you don't have to worry about different transform properties or collapsed transformations.
To simplify working with 2.5D layers: When working with a 2D layer that has a 3D effect on it (i.e. a 2.5D layer), that's supposed to be integrated into a 3D scene, you might have to split the 2.5D layer at some point because it has to go from behind another 3D layer to before it. You can create a Clone in Comp from the 2.5D layer, split source and clone (see Clone Creation Options), and have a live copy of the source layer. Another example would be the other way around: You have a 3D layer that has to interact with a 2D layer and at some point, it has to go from behind to before or the other way around. You can also split source and clone by opacity, meaning that the source layer can still be grabbed and moved around in the composition panel, even when a clone layer is active at that time. 
To intensify a layer: When creating a glow, for example, you might want to duplicate a layer, apply a blur to it and repeat this process several times to create a unique result. When changes are made on the source layer, however, they won't update on the duplicated layers. That's when a Clone in Comp can come in handy as a more flexible way to duplicate a layer.
Disadvantages of a Clone in Comp
There are also some drawbacks when using a Clone in Comp:
You can only clone one layer, so it's not possible (like when using a Precomp Clone) to merge several layers on one clone layer. Besides, you can't clone shape and text layers. Also, as of now, it's not possible to use custom transforms on a Clone in Comp. (In the current Workflower build, to transform a Clone in Comp, you can use AE's Transform effect on the clone layer. This, however, only works with 2D transforms.)
Clone Creation Options
Clone in Comp Dialog
Cloning Channels
You can choose to either clone RGBA or clone Alpha Only. Cloning Alpha Only using the Set Matte effect has three advantages compared to cloning RGBA using the Calculations effect:
1.It is faster since the Set Matte effect is GPU accelerated.
2.Set Matte supports 32 bit, while Calculations only supports 16 bit.
3.You can extend borders of the clone layer dynamically using the dedicated slider, while, using the Calculations effect, the layer needs to be precomped in order to extend the borders.
Precomp Source & Expand Border
In certain situations, you might want to extend the borders of a clone layer. For example, when you apply a blur or some other effect that stretches pixels beyond the layer's boundaries. On Clones in Comp with a Set Matte effect, you simply need to use the Expand Borders slider on the Clone in Comp Settings effect. On Clones in Comp with a Calculations effect, you can, when creating the clone, automatically precomp the source and expand the border by a certain percentage. That way, the layer will have empty pixels around its boundaries onto which a blur, for example, can stretch pixels. When using Precomp Source & Expand Border, all transform properties of the layer will be adjusted in such a way that the image itself will stay at exactly the same position, even when keyframes were applied.
Split Source & Clone at Current Time
When dealing with 2.5D layers, it can be useful to split the source and clone layer at a given time so that the source layer becomes invisible once the clone layer becomes visible. Check this checkbox to quickly execute this action. Examples, when this can be useful, are listed under Advantages of a Clone in Comp.
Clone Settings
Clone in Comp Settings Effect
On the source layer, an effect will be added. On it, you can customize various settings:
How the opacity of the clones should behave: either it's a custom opacity on each clone, or a custom opacity set for all clones on the settings effect, or it's linked to the source layer opacity.
If you choose to use a custom opacity on each clone, you need to modify the clone's opacity on the slider of the dedicated effect on the clone layer, not AE's opacity slider. (This slider will have an expression applied to it and is therefore not usable anymore.) You can execute Reveal Layer Opacity to reveal the slider in the timeline, too.
Clone in Comp Opacity Slider
Whether you want to link the in/out point and/or the blending mode to the source layer.
Whether and by how much you want to expand the clone's borders (see Precomp Source & Expand Border chapter for more information).
​
Show Clone Layers
Shows layers, contained in a Prime Clone, while hiding the Prime Clone layer itself, or vice-versa (Win: Ctrl+Shift+Return, Mac: macControl+Return).
For more information on working with Prime Clone layers, see its chapter. 
Using Show Clone Layers is a faster way to show/hide Prime Clone layers than clicking on the checkbox of the Precomp Clone's effect.
When hiding Prime Clone layers, Quick Refresh Connections will be executed to refresh all clone layers. This can be deactivated, too, by going to the Cloning Settings.
Preview Custom Clone Size
Previews the new boundaries of a Precomp Clone with custom size (not available via shortcut; Win: Alt+Click on the Cloning Button; Mac: Option+Click on the Cloning Button).
Preview Border of the new Custom Clone Size
Use the Custom Size sliders on the Precomp Clone effect to define the new clone size and the preview - that's linked by expressions to the sliders - will live-update its border. When you're done, hit Refresh Connections to apply the new size. After applying, the preview will disappear. If the preview is active but you decide not to apply a custom size, just hit Refresh Layout to remove the preview.
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Outline
Clone and Precomp
Refreshing Layer Attributes
Duplicating a Precomp Clone
Adding / Removing Clone Layers
Unlink Properties
Prime Clone
Group Clone
Custom Layer Order
Custom Precomp Size
Enabling Precomp Transforms
Custom Clone Layer States
3D Precomp Clones [Experimental]
Clone and Precomp Modes
Clone in Comp
Advantages of a Clone in Comp
Disadvantages of a Clone in Comp
Clone Creation Options
Clone Settings
Show Clone Layers
Preview Custom Clone Size