Update lockfile for manifest cleanup

Refresh Cargo.lock after removing stale dependency declarations from the extraction refactor.

Co-authored-by: Codex <noreply@openai.com>

codex-rs/Cargo.lock

@@ -1647,7 +1647,6 @@ dependencies = [
  "thiserror 2.0.18",
  "tokio",
  "toml 0.9.11+spec-1.1.0",
- "toml_edit 0.24.0+spec-1.1.0",
  "tracing",
  "url",
  "zip",
@@ -1892,7 +1891,6 @@ dependencies = [
  "codex-secrets",
  "codex-shell-command",
  "codex-shell-escalation",
- "codex-skills",
  "codex-state",
  "codex-terminal-detection",
  "codex-test-macros",