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/util/alignment.py

@@ -56,7 +56,7 @@ def append_zero_length_segments(file: ifcopenshell.file) -> ifcopenshell.file:
     for alignment in alignments:
         layouts = ifcopenshell.api.alignment.get_alignment_layouts(alignment)
         for layout in layouts:
-            ifcopenshell.api.alignment.add_zero_length_segment(patched_file, layout, include_referent=False)
+            ifcopenshell.api.alignment.add_zero_length_segment(patched_file, layout)
             curve = ifcopenshell.api.alignment.get_layout_curve(layout)
             if curve:
                 ifcopenshell.api.alignment.add_zero_length_segment(patched_file, curve)