I cannot find the mcon layer in magic, where is the mapping of the Skywater layers to the magic layers documented?

Those are vias - Magic handles vias as a specification of both the "from" and "to" layers. They're the drawing tools with large Xs in the palette.

@Philipp Gühring: This document: https://docs.google.com/spreadsheets/d/1oL6ldkQdLu-4FEQE0lX6BcgbqzYfNnd1XA8vERe0vpE/edit#gid=0 on the sheet "Magic DRC rule mapping", has a list of skywater layer vs. magic layer. Unfortunately, that page is deprecated and the new page outlining the DRC rule mapping does not list the layers in magic. I will need to add some documentation.