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/skill_manager_tool.py

@@ -780,7 +780,7 @@ def skill_manage(
             if action == "create":
                 if is_background_review():
                     mark_agent_created(name)
-            elif action in ("patch", "edit", "write_file", "remove_file"):
+            elif action in {"patch", "edit", "write_file", "remove_file"}:
                 bump_patch(name)
             elif action == "delete":
                 forget(name)