Michael,

> Try calling factory.disableUIGeometry(); before the generate fragments call,
> that should manually set the flag that disables UI geometry so I think that
> would then prevent those extra things from being created.

I tried modifying the 'trim' function to be:

var trimmer = factory( 'trim', as_list( objects ), as_list( cutters ), 
                       object_list(), 'remove', arg( extend_lines, false ), 
                       arg( project_intersections, true ) );
trimmer.disableUIGeometry();
var result = trimmer.generateFragments();
var result = trimmer.calculate();
trimmer.reset();

but it did not have any effect on the problem. Note that the geometry I see all seems correct and expected. The problem is simply that the UI seems to be 'stuck' in some kind of picking mode at the end of the script. Pressing esc seems to end the picking mode and return everything to normal.