Make generate_bead_model use one_bead_per_monomer=True by default with max 1 bead per nt and bp, otherwise False

Order of double-stranded segment creation and ds-segment direction should match original cadnano reader.
Position and orientation of cadnano bases more consistent with original cadnano reader.

Fix bug handling insertions and skips at strand ends; handle multiple consecutive skips; in model_from_lists, convert terminal_crossover dsDNA-dsDNA connections to intrahelical when nearby crossovers exist between the two segments