Hello I'm perusing the javascript source code of the simulator and would like to make some suggestions. Adding a few comments at the beginning of some files would make them much easier to understand.

1. The segdefs file(these are the node definitions I suppose): https://raw.github.com/trebonian/visual6502/master/segdefs.js. I assume the format is the following:
[Node Nr., '+' for powered '-' for neutral or ground, a polygon which is part of the node]
If the node is composed of more polygons the above line is repeated one for each polygon.

2.The transdefs file(these are the transistor definitions): https://github.com/trebonian/visual6502/blob/master/transdefs.js. From the code I deduced the following:
[transistor name starting with a 't', gate node, source node, drain node, [bounding box?], [no idea what this is]]
I'm not sure about source node and drain node since they seem to be interchangeable. In the source I saw the variables c1 and c2 being used to name them.

If my comments are correct I would suggest adding them to the source code.

You're right on all counts!

Ed