Fix ty-ios type-check errors (ifcopenshell-python side)

poe ty's sequence only reaches ty-ios once ty-bonsai passes, so these
never surfaced until now:

- util/alignment.py: drop the stale `include_referent=False` kwarg from
  add_zero_length_segment() - that parameter was removed from the function's
  signature in 45ea5eb07 but this caller in a different file was missed,
  leaving a latent TypeError if this code path is ever exercised.
- ifcopenshell_wrapper.pyi: add the optional trailing `logger` parameter to
  parse_ifcxml/open/construct_iterator*, matching the real SWIG signatures
  in src/ifcwrap/*.i (all declare `Logger& logger = Logger::Root()`) that
  the hand-maintained stub never picked up.
- ifcopenshell/__init__.py: remove a stale `ty: ignore[unknown-argument]`
  comment that ty confirms is no longer suppressing anything.
- assign_cost_item_quantity.py: OPERATORS mixes 2-arg binary operators with
  the 1-arg `operator.neg` (for ast.USub), but FormulaEvaluator has no
  visit_UnaryOp so USub can never reach this lookup via visit_BinOp.
  Suppressed at the call site rather than touching the dict, since this
  looks like scaffolding for unary-minus support rather than dead code.
- Explicit submodule imports (ifcopenshell.geom / api.alignment / util.unit
  / api.aggregate / api.context / api.spatial) added where accessed but
  only reachable by accident of import order.

(cherry picked from commit d5e890bccd)

src/ifcopenshell-python/ifcopenshell/__init__.py

@@ -249,7 +249,7 @@ def open(
         kwargs = {"mmap": mmap}
         if logger is not None:
             kwargs["logger"] = logger
-        f = ifcopenshell_wrapper.open(str(path.absolute()), **kwargs)  # ty: ignore[unknown-argument]
+        f = ifcopenshell_wrapper.open(str(path.absolute()), **kwargs)
     else:
         f = ifcopenshell_wrapper.open(str(path.absolute()), False, *optional_logger_args(logger))