Was wondering if there is an automated way to re-position shapes to minimize the space between them. Besides manually trying to guess the optimal configuration.
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The feature you are describing is called "nesting" and Illustrator does not have a native way to do this. It requires special plugin software that you can buy separately. – 13ruce Mar 10 '20 at 16:59
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Manual placing is easy in Inkscape. There the bounding box contains the stroke and snap to bounding box is possible. Let objects have a stroke and drag them to lean against each other. Select all, remove the stroke => objects have equal gaps between them – user287001 Mar 10 '20 at 19:52