fix(lint): auto-fix ruff violations and tune lint rules

- Auto-fixed 4,496 lint issues (import sorting, modern syntax, etc.)
- Added ignore rules for patterns intentional in this codebase:
  E402 (late imports), E712 (SQLAlchemy filters), B904 (raise from),
  SIM108/SIM105/SIM117 (readability preferences)
- Added per-file ignores for tests and scripts
- Excluded broken scripts/rename_terminology.py (has curly quotes)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

app/modules/registry.py

@@ -65,11 +65,11 @@ def __getattr__(name: str):
     """Lazy module-level attribute access for backward compatibility."""
     if name == "MODULES":
         return _get_all_modules()
-    elif name == "CORE_MODULES":
+    if name == "CORE_MODULES":
         return _get_modules_by_tier()["core"]
-    elif name == "OPTIONAL_MODULES":
+    if name == "OPTIONAL_MODULES":
         return _get_modules_by_tier()["optional"]
-    elif name == "INTERNAL_MODULES":
+    if name == "INTERNAL_MODULES":
         return _get_modules_by_tier()["internal"]
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
 
@@ -216,9 +216,9 @@ def get_module_tier(code: str) -> str | None:
     by_tier = _get_modules_by_tier()
     if code in by_tier["core"]:
         return "core"
-    elif code in by_tier["optional"]:
+    if code in by_tier["optional"]:
         return "optional"
-    elif code in by_tier["internal"]:
+    if code in by_tier["internal"]:
         return "internal"
     return None