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.

src/ifcopenshell-python/ifcopenshell/ifcopenshell_wrapper.pyi

@@ -1697,10 +1697,16 @@ class uninitialized_tag: ...
 
 def arrange_polygons(settings, polygons): ...
 def clear_schemas(): ...
-def construct_iterator(geometry_library, settings, file, num_threads): ...
-def construct_iterator_with_include_exclude(geometry_library, settings, file, elems, include, num_threads): ...
-def construct_iterator_with_include_exclude_globalid(geometry_library, settings, file, elems, include, num_threads): ...
-def construct_iterator_with_include_exclude_id(geometry_library, settings, file, elems, include, num_threads): ...
+def construct_iterator(geometry_library, settings, file, num_threads, logger=...): ...
+def construct_iterator_with_include_exclude(
+    geometry_library, settings, file, elems, include, num_threads, logger=...
+): ...
+def construct_iterator_with_include_exclude_globalid(
+    geometry_library, settings, file, elems, include, num_threads, logger=...
+): ...
+def construct_iterator_with_include_exclude_id(
+    geometry_library, settings, file, elems, include, num_threads, logger=...
+): ...
 def convert_loop_to_function_item(loop): ...
 def create_box(*args): ...
 def create_epeck(*args): ...
@@ -1717,8 +1723,8 @@ def line_segments_to_polygons(s, eps, segments): ...
 def map_shape(settings, instance): ...
 def nary_union(sequence): ...
 def new_IfcBaseClass(schema_identifier: str, name: str) -> entity_instance: ...
-def open(fn: str, readonly: bool = False) -> file: ...
-def parse_ifcxml(filename): ...
+def open(fn: str, readonly: bool = False, logger=...) -> file: ...
+def parse_ifcxml(filename, logger=...): ...
 def polygons_to_svg(*args): ...
 def read(data): ...
 def register_schema(arg1): ...