- fix off-by-one errors
- fix stop codon bug
- replace elements_ in Polymer with IntervalMap
- add promoters_
- add terminators_
- remove sorting code
- simplify overlap lookups in Polymer for move ops
- simplify overlap lookups for binding in Polymer
- convert SpeciesTracker from singleton to pass by arg
- remove "shared from this" from as many classes as possible
- add _total counts back in
- simplify/refactor signalling
- have objects query other objects directly for actions
- docs: getting started tutorial