Improve loop.plot

[jeanluct]

loop.plot is a bit of a mess, still (despite issue #1).

In writing the taffy puller paper, I find I need more flexibility in specifying the spacing. Right now, the puncture size can be adjusted, but it doesn't adjust the position of the loops around the punctures. All this needs to be specified using options.

[jeanluct]

Another improvement requested by John Lynch: optionally fill the space inside a loop. This probably requires a handle, as required by #141.

(Moved this to a new separate issue, #144.)