ci: mypy ratchet -- keep type-clean modules clean (71 modules, 536 -> 442 errors) (#661)

* ci: mypy ratchet -- keep type-clean modules clean

mypy-clean.txt lists the 71 modules under src/ that type-check clean;
scripts/check_types.py runs mypy (--follow-imports=silent) on exactly
those files and fails on any error or a missing/unsorted/duplicate entry.
A new "Type check (mypy ratchet)" CI job runs it with mypy 1.20.2 and
pinned stubs; the manual pre-commit mypy hook now runs the same script
(a local hook, so mypy sees the installed requirements like CI does).

35 modules were made clean with annotation-only fixes: hints, typing.cast,
TYPE_CHECKING imports, implicit-Optional defaults made explicit, and
annotations widened (never guards removed) where mypy called a defensive
isinstance check unreachable. No runtime behaviour change.

mypy.ini: numpy and orjson are treated as Any (follow_imports=skip, also
for stubs). numpy 2.3+ stubs use 3.12 `type` statements that mypy won't
parse at python_version 3.10, and orjson is optional, so seeing its stubs
made the result depend on whether it was installed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* chore: annotate check_types.py's list-form mypy subprocess

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

src/logging_config.py

@@ -125,6 +125,7 @@ def setup_logging(
     root_logger.handlers.clear()
     
     # Create formatter based on type
+    formatter: logging.Formatter
     if format_type == 'json':
         formatter = StructuredFormatter()
     else:
@@ -244,7 +245,7 @@ class PluginLoggerAdapter(logging.LoggerAdapter):
 
     def process(self, msg, kwargs):
         extra = dict(kwargs.get('extra') or {})
-        extra.setdefault('plugin_id', self.extra.get('plugin_id'))
+        extra.setdefault('plugin_id', self.extra.get('plugin_id'))  # type: ignore[union-attr]  # get_logger always passes a dict
         kwargs['extra'] = extra
         return msg, kwargs
 
@@ -290,7 +291,7 @@ def log_with_context(
         operation_id: Optional operation ID for request tracking
         exc_info: Optional exception info for error logging
     """
-    extra = {}
+    extra: Dict[str, Any] = {}
     
     if context:
         extra['context'] = context