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I just happened to be writing an addition to the manual for managing layers - specifically filtering the list. An available option that may help you is the ability to filter the layer list. It doesn't group the layers or change the order, but narrows the list that is shown in the dock.
In the input box at the top of the Layer List dock, type a list name, or partial list name. Wildcards (* for multiple characters, ? for a single character) can also be used in the filter string. Typing "main" will list all layers starting with "main"; main_layer_01, main_layer_02, etc. Typing "*layer_02" will list layers main_layer_02, option1_layer_02, option2_layer_02, etc. Putting "option?_layer_0" in the filter will list to option1_layer_01, option1_layer_02, option2_layer_01,
option2_layer_02, ...
I hope that is helpful..
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