Any reason why when I merge some subtools using the SubTool Master, it goes 3 steps back in the history on every subtool? How can I avoid/deal with that?
You can try isolating your subtools by making them Visible and hide what you don't need and then push Merge Visible, that will create a different tool with your merged subtools. And you don't need to use Master at all...
But why it does what you say it does, I have absolutely no idea
The issue with that work flow is that it doesn't attempt to preserve subdivision levels of the subtools . And yeah, the undo thing seems totally arbitrary...
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But why it does what you say it does, I have absolutely no idea