Puppet Warp should respect existing layer structures.
I love Puppet Warp but I hate having to ungroup my paths and put them back in the layer structure that works for me when I'm done using Puppet Warp.
Please do whatever needs to be done so that I can grab a bunch of paths about multiple layers, Puppet Warp them, and have them stay in the same place they were before I did this. I'm fine if it's a switch in the tool's settings because some people love this behavior.
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A workaround is to use a script by Sergey Osokin:
https://github.com/creold/illustrator-scripts/blob/master/jsx/RememberSelectionLayers.jsx
Should be run before using Puppet Warp or Free Transform tools for objects on different layers and then again after completing.
Won’t work with sublayers. -
Margaret Trauth
commented
I'm still really annoyed by this whenever I have to deal with it. Why on earth does this tool think it's acceptable to completely trash my layer structure.
Who thought this was ever a good idea. How happy would you be if your text editor thought it was a great idea to cram the contents of ten source files into one when you did a certain action? You'd hate it.
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A related request:
Free transform tool groups selected layers to one layer
http://illustrator.uservoice.com/forums/601447/suggestions/46477726