security: add a dependency audit command and CI gate

[WalksWithASwagger]

Summary

Add one explicit security-verification command and CI gate for root npm, frontend npm, and locked Python dependencies.

Context

• Blocked by build: add a reproducible hashed Python 3.11 CI lock #329.
• Roadmap phase: Phase 1 - dependency health
• Relevant files: root package.json, .github/workflows/ci.yml, Python audit tooling/configuration, and focused workflow tests
• Current behavior: deterministic tests run, but dependency vulnerability checks are incomplete or split across ad hoc commands; the frontend graph is not consistently audited.
• Desired behavior: npm run verify:security performs the documented networked dependency checks and CI fails on actionable high-severity findings.

Implementation Notes

• Audit the root production npm graph, the frontend production graph, and the hashed Python CI lock.
• Include frontend build dependencies in a separate visible check because Vite-related advisories can live outside the production-only tree.
• Do not use npm audit fix --force or silently suppress an advisory.
• Separate deterministic npm run verify from networked verify:security in documentation and CI.

Acceptance Criteria

• npm run verify:security runs root production npm audit, frontend production npm audit, frontend full-tree audit, and pip-audit against the CI lock.
• CI invokes the command in a clearly named dependency-security step.
• High-severity findings fail unless a specific, scoped, documented exception is reviewed.
• Any upstream-only deprecation is named and tracked without forcing an unrelated framework upgrade.
• No audit command mutates lockfiles or installs globally.
• The deterministic local verification command remains network-independent.

Tests/Evals

• Add workflow/script tests that protect command composition and failure propagation.
• Use registry/network access only for the audits themselves; never invoke providers.

Verification

• npm run verify
• npm run verify:security
• python3 -m pytest tests/agentic/test_workflows.py -q
• git status --short after verification shows no generated or lockfile changes.

Agent Instructions

• Use branch codex/issue-<this-issue>-dependency-security-gate.
• Do not start until build: add a reproducible hashed Python 3.11 CI lock #329 is merged and main is green.
• Never use forced audit remediation or broad dependency upgrades.
• If an advisory cannot be resolved safely, report it with exact dependency-path evidence and stop.

Human Checkpoints

• Maintainer review is required before accepting any temporary high-severity exception.

Out of Scope

• Major framework upgrades.
• GitHub Action pinning, Dependabot, CodeQL, or dependency-review workflows.
• Automated dependency merging.
• Provider calls or credential changes.

Linear

Not applicable. Rafiki delivery is GitHub-only; do not create or update a Linear issue.