[FIX] PR #162: verify sync_command_count.py was run (not manual count bump)

[Wolfvin]

Context

PR #162 (feat(deps-audit): dependency vulnerability scan via OSV.dev API — closes #158) appears to have manually edited command counts in README.md, SKILL.md, and other files, rather than running sync_command_count.py --apply.

Issue

The PR bumps counts to 71 commands / 69 MCP tools. This may be correct, but needs to be verified by the automated script — not a manual edit.

Fix

1. Rebase PR feat(deps-audit): dependency vulnerability scan via OSV.dev API (closes #158) #162 on main (main has moved significantly since this PR was opened)
2. Run python3 scripts/sync_command_count.py --apply
3. Commit if the script produces different numbers than what's in the PR
4. Push the rebased + corrected branch

Definition of Done

• PR feat(deps-audit): dependency vulnerability scan via OSV.dev API (closes #158) #162 rebased on latest main
• sync_command_count.py --apply run — output counts match docs files
• If counts differ: corrected counts committed
• PR feat(deps-audit): dependency vulnerability scan via OSV.dev API (closes #158) #162 is mergeable

[Wolfvin]

🔄 Taking this issue

Mengerjakan issue ini -- 2026-07-03T02:55:22Z

Scope: full issue — verify sync_command_count.py --apply was run on PR #162 (deps-audit), and fix any manual count edits if found.

[Wolfvin]

PR siap review

PR: #162 — fix(deps-audit): rebase on main + run sync_command_count.py (closes #172)
Branch: feat/issue-158-deps-audit-osv (force-pushed with rebased history)
Summary: Rebased PR #162 on latest main (was 39 commits behind). Resolved 6 doc-file conflicts (all command-count numbers — took main's version then re-applied my changes: graph_model constants, README/SKILL-QUICK deps-audit rows). Ran sync_command_count.py --apply — counts corrected from 71→76 commands / 68→74 MCP tools (delta from other merged PRs: orient #165, large-file-threshold #163, etc.). sync_command_count.py --check now reports "All documentation files are in sync with COMMAND_REGISTRY".
Tests: 47 passed, 0 skipped, 0 failed (test_deps_audit.py)

Note: codelens.py --command-count crashes with argparse 'conflicting option string: -f' — pre-existing bug in main (the affected command defines -f --filter which conflicts with the global --format -f alias). NOT fixed here (out of scope for #172). sync_command_count.py works fine when invoked directly because it imports COMMAND_REGISTRY without going through codelens.py main.