The code that removes duplicate lines from svg paths in 3d/scripts/svg_processor.py has a problem. When I run generate_2d.py, the output in combined.svg looks like this:

The diagonal lines cutting across some of the parts are caused by trimming lines immediately preceding Close elements from some of the paths. When the svg.path package parses an svg path and returns a representation, Close elements are returned with a start and end point, just like a Line element. But the XML representation of Close is just a Z, which is interpreted by svg editors as, 'draw a line from the current point to the location of the most recent Move element in this path.' As a result, even though the path removal code was updating the start or end points for the Close element after it removed the preceding line, those points were just being ignored when svg.path regenerated the XML for the altered path.

I have a fix for this problem, which is just to turn all Close elements into Line elements when processing paths. The resulting .svg files have worked fine in both svg editors (inkscape and Affinity Design, at least), and when used to drive my Glowforge. I'll submit a PR with those changes in a few minutes.