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When an SVG has layers that are grouped by <g> tags with id attributes, saxi will be able to split layers according to the group ID, instead of the default layering logic of separating layers by stroke color.
By default, if a drawing has multiple stroke colors, saxi will guess that you want to split the drawing into layers according to the stroke color, since that's what it used to do, and you might have adapted your workflow to that. If there's no stroke information, or if there's only a single stroke color, saxi will guess you want to split by group IDs instead.
If saxi makes the wrong guess, you can help it out by switching the 'layer by group' option under 'more' in the plot settings.
Thanks to @abey79 for this suggestion as well (#40).