chore: ruff auto-fix PLR6201 — tuple → set in membership tests (#23937)

Replace  with  for all literal-tuple
membership tests. Set lookup is O(1) vs O(n) for tuple — consistent
micro-optimization across the codebase.

608 instances fixed via `ruff --fix --unsafe-fixes`, 0 remaining.
133 files, +626/-626 (net zero).

tools/checkpoint_manager.py

@@ -639,7 +639,7 @@ class CheckpointManager:
         abs_dir = str(_normalize_path(working_dir))
 
         # Skip root, home, and other overly broad directories
-        if abs_dir in ("/", str(Path.home())):
+        if abs_dir in {"/", str(Path.home())}:
             logger.debug("Checkpoint skipped: directory too broad (%s)", abs_dir)
             return False