Improve implementations of new bond formations between Ports

[timbernat]

• bonding.substitution : implement capping such that newly-inserted atoms in cap groups are appended to the list of atom ids, rather than mixed in (i.e. reimplement hydrogenate_mol_ports and saturate_ports to preserve initial atom order via Chem.rdmolops.RenumberAtoms)
• Re-implement increase_bond_order to change bond in "one-shot" (rather than by iterating single-order upconversions). This would remove the need to relocate atom IDs by map number after each upconversion and would simplify sanitization
  • Canonicalize alternate implementation of _increase_bond_order backend method