Is there a simple and free application for 'designing' a prototype shield (like this?)
Currently I use Excel and a 'Above' and 'Below' side next to each other but it gets messy already with such a small shield layout.
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Outside the Arduino world, that is called a Printed Circuit Board (PCB).
We use electronic CAD programs to draw the schematic diagram and lay out the the PC board. The CAD program will produce Gerber photoplot files and NC drill files that a PCB shop can use to make the final boards.
Two CAD programs often used are Eagle and KiCAD.