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>

scripts/show_structure.py

@@ -23,7 +23,7 @@ def count_files(directory: str, pattern: str) -> int:
         return 0
 
     count = 0
-    for root, dirs, files in os.walk(directory):
+    for _root, dirs, files in os.walk(directory):
         # Skip __pycache__ and other cache directories
         dirs[:] = [
             d