Impl. taxaSPAdes as option with --taxonomy as argument & some clean-up

config.info:
- Added taxonomy false.

barcode_index_builder.hpp:
- only extract TaxaTree if cfg::get().taxonomy

scaffold_graph_construction_pipeline.cpp:
- only add TaxaBreak constructor if cfg::get().taxonomy

config_struct.cpp & hpp:
- added taxonomy to cfg.

barcode_index_construction.cpp:
- Only decide LCA if cfg::get().taxonomy

spades_iteration_stage.py:
- Add taxonomy option to config.info of final iteration

options_parser.py:
- Add --taxonomy argument. Only usable with --meta and --gemcode options.

Some various other clean-ups in files:
- aa_todo_notes
- path_polisher.hpp
- path_scaffolder.cpp
- scaffold_vertex.cpp

Signed-off-by: Overduin, Sam <sam.overduin@wur.nl>