Files
ruflo/verification
rUv 402b701a9d fix(security): ADR-165 Phase 1 — close 5 critical CVEs + refresh registry + audit CI gate (#2508)
* fix(security): ADR-165 Phase 1 — close all critical CVEs, refresh registry, add CI gate

Closes ADR-165 Phase 1. Both workspaces pass `npm audit --audit-level=critical`.

## Before (2026-06-29)

| Workspace | Critical | High | Moderate | Total |
|-----------|----------|------|----------|-------|
| Root      | **1**    | 6    | 31       | 38    |
| v3        | **4**    | 33   | 57       | 97    |

## After

| Workspace | Critical | High | Moderate | Total |
|-----------|----------|------|----------|-------|
| Root      | **0**    | 0    | 31       | 31    |
| v3        | **0**    | 27   | 58       | 88    |

All 5 critical advisories closed (vitest GHSA-5xrq, handlebars prototype-pollution,
protobufjs constructor-pollution, plus 2 more in v3). 12 of 39 high advisories
closed via overrides; the remaining 27 v3 highs are deeper transitive chains
that would require breaking-change major bumps — flagged for ADR-165 Phase 2.

## Changes

### Root workspace overrides (package.json)

- `vitest`: `^1.0.0` → `^3.2.6` (closes critical GHSA-5xrq CVSS 9.8)
- `hono`: `>=4.11.4` → `>=4.12.25` (closes 6 hono advisories)
- `undici`: `>=7.18.0` → `>=8.5.0` (closes 7 undici advisories — bumps the
  stale pin that ADR-165 flagged as still-in-vulnerable-range)
- `vite`: `>=6.4.6` → `>=8.0.16` (closes 2 vite advisories)
- NEW `@grpc/grpc-js`: `>=1.14.4`
- NEW `form-data`: `>=4.0.6`
- NEW `http-proxy-middleware`: `>=3.0.7`
- `@hono/node-server`: `>=1.19.10` → `>=1.19.14`

### v3 workspace overrides (v3/package.json + pnpm.overrides)

- `vitest`: `^4.0.16` → `^4.1.0` (and `@vitest/coverage-v8` matched)
- Top-level + pnpm overrides: `handlebars: >=4.7.9`, `protobufjs: >=8.6.0`
- 27 sub-package `package.json` updated to `vitest ^4.1.0`

### CVE registry refresh (v3/@claude-flow/security/src/CVE-REMEDIATION.ts)

Rewritten from 5 stale Jan-2026 entries to 16 total: 15 fixed, 1 open
(ADR165-OPEN-01 — PII pipeline wiring per ADR-164 §6.1 not yet on
dispatch-layer). `SECURITY_SUMMARY` is now computed dynamically from the
registry; `validateRemediation()` correctly returns `allFixed: false`
with 1 issue. ADR-165 §5 flagged this as THE Phase 2 priority — now closed.

### New CI gate

`.github/workflows/cve-audit.yml`:
- `audit-root` — `npm audit --audit-level=critical` in root, blocking
- `audit-v3` — same in v3, blocking
- `audit-high-report` — warn-only summary on high-severity drift
- Triggers: PR, push to main, daily cron

### ADR-165 §9 evidence ledger addendum

Captures AFTER-remediation `npm audit --json` metadata for both workspaces.
The diff between BEFORE (already in §9) and AFTER makes Phase 1 verifiable.

Also CORRECTED one prior surprise in §9: the `validate-input.ts` in
`mcp-tools/` is NOT a 9-line shim. It's 269 lines of real implementation.
(That was an inaccurate findings note from the initial audit.)

### §7.3 research items resolved

- `protobufjs` v3 chain confirmed gone after override pins
- `handlebars` v3 chain confirmed not user-reachable on the workflow path
  (toolchain-only; override sufficient)
- `validate-input.ts` confirmed real implementation, not a shim (registry
  entry corrected)
- CORS surface check: no `cors()` / `app.use(cors` call sites — the hono
  CORS-wildcard advisory is not exploitable on the current server
- ADR-164 §6.1 PII pipeline NOT wired in current agentbbs dispatch —
  recorded as ADR165-OPEN-01 (Phase 3 work)

## Gates (all PASS)

- `npm audit --audit-level=critical` root: exit 0 (was non-zero)
- `npm audit --audit-level=critical` v3:   exit 0 (was non-zero)
- vitest suites: 105/109 pass (4 skip-conditional — same as before)
- ADR-112 audit: 352/352 tools with guidance
- business-pods smoke: 11/11 PASS
- agentbbs smoke: 8/8 PASS
- agenticow smoke: 8/8 PASS
- cli build: clean (tsc)

## Phase 2+ deferred

The 27 v3 high-severity advisories that remain are transitive chains with
no patched-in-range version. ADR-165 §6 Phase 2 picks these up after the
`cve-watch.yml` automation in §6 lands (NEW PR — not in scope here).

Co-Authored-By: RuFlo <ruv@ruv.net>
Claude-Session: https://claude.ai/code/session_01WbBa4nccx5aGhXphoHxcni

* chore(lock): regen v3/pnpm-lock.yaml after override updates (PR #2508 CI fix)

PR #2508 added handlebars + protobufjs to v3 overrides + bumped vitest pin,
but v3/pnpm-lock.yaml wasn't regenerated. CI surfaced
ERR_PNPM_LOCKFILE_CONFIG_MISMATCH on every install step.

Same pattern as the previous lockfile-drift fixes on PR #2500 and #2503.

* fix(ci): cve-audit.yml jq-only + regen witness manifests for #1609 marker drift

Two PR #2508 CI failures fixed:

1. Static-regression-guard tripped on cve-audit.yml line 52: the static
   YAML strict-parser sees `if high > 0:` inside the `run: |` block as
   a YAML block-mapping key indicator. Refactored all 3 inline-python
   blocks to use jq (preinstalled on ubuntu-latest) — no embedded
   `if x > 0:` lines, so the YAML guard passes.

2. Witness marker drift smoke flagged fix-marker #1609 — the Phase 1
   vitest bump (4.0.16 → 4.1.0) drifted the cited marker string in
   v3/@claude-flow/aidefence/package.json. Updated `marker` field in
   all 3 platform manifests + `desc` to reference ADR-165 Phase 1, then
   re-signed via plugins/ruflo-core/scripts/witness/regen.mjs.

Co-Authored-By: RuFlo <ruv@ruv.net>
2026-06-29 22:41:24 -04:00
..

Ruflo Verification System

A cross-platform, cryptographically-signed regression-protection toolkit. Every documented fix in ruflo gets attested by a SHA-256 + marker substring + Ed25519 signature. Anyone with the same git commit can re-derive the public key and verify it independently.

Three-layer regression protection:

  1. Behavioral smoke tests (CI) — exercise user-visible failure modes
  2. Cryptographic witness manifest (this folder) — attest fix presence
  3. Temporal history (<os>/history.jsonl) — bisect when a regression was introduced

See docs/validation/README.md for the full architecture, ADR-102 for the smoke-harness pattern, and ADR-103 for the temporal-history layer.


Why this exists

Three regressions filed on 2026-05-08 (#1859, #1862, #1867) all passed unit tests on the broken commits but broke for users on first install. Unit tests verify code paths; users hit subprocess flag parsers, fresh npm install resolution, plugin/CLI version drift. The witness layer attests that every documented fix's load-bearing code is still present — even when the fix has no dedicated smoke test.

A regression that deletes the load-bearing line of a fix flips its markerVerified to false. The CI's witness-verify job blocks publish.


Folder layout

verification/
  README.md                  ← you are here
  witness-fixes.json         ← input config (OS-independent)
  mcp-tool-baseline.json     ← ADR-112 — monotone-decreasing tool-discoverability baseline
  results.md                 ← human-readable last-run report
  inventory.json             ← reserved for capability inventory
  linux/
    manifest.md.json         ← signed by Linux CI runner
    history.jsonl            ← Linux temporal log
  macos/
    manifest.md.json         ← signed by macOS CI runner
    history.jsonl            ← macOS temporal log
  windows/
    manifest.md.json         ← signed by Windows CI runner
    history.jsonl            ← Windows temporal log

Why per-OS? File hashes drift across platforms (LF vs CRLF normalization, path separators, prebuilt binary differences). Each OS produces its own truthful snapshot. The witness-verify CI job runs once per OS and writes/verifies that OS's bundle, catching platform-specific marker drift before it reaches users on that platform.

Why JSONL inside each OS folder? The witness use case is structured key-value retrieval (snapshot N's commit + fix statuses), not vector similarity search. JSONL is git-diff-friendly, append-cheap, and human-readable — the better fit. The folder layout adopts the RVF-style cognitive container concept (per-OS bundle of manifest + history + metadata); the file format inside is JSONL.


Tutorial — adopt the witness in your own project

1. Bootstrap

The witness toolkit lives in plugins/ruflo-core/scripts/witness/ — copy it into your project (or install the ruflo-core plugin).

# Initialize per-OS folders + sample fix template
node plugins/ruflo-core/scripts/witness/init.mjs --root .

# Single runtime dependency
npm i @noble/ed25519

Outputs:

verification/
  witness-fixes.json     # template — edit with your fixes
  <os>/
    manifest.md.json     # empty seed
    history.jsonl        # empty seed

2. Register your first fix

Open verification/witness-fixes.json:

{
  "fixes": [
    {
      "id": "MY-001",
      "desc": "Race condition in token refresh — early-return on in-flight refresh",
      "file": "dist/auth.js",
      "marker": "if (this._refreshing) return this._refreshing;"
    }
  ]
}

Choosing a marker is the load-bearing skill:

Bad marker Why it fails
'function' False-positives in any file with a function
'TODO' Flaps as TODOs come and go
'fix' Too generic
Good marker Why it works
(await import('better-sqlite3')).default Distinctive AND specific to the fix mechanism
(ctx.flags.file as string) || ctx.args[0] The exact swap that fixes the bug
import * as bcrypt from 'bcryptjs' Proves the bcrypt → bcryptjs migration is in dist

Pick a unique substring from the diff that's specifically created by the fix.

3. Generate the signed manifest

In ruflo's monorepo there's a wrapper that hard-codes paths:

node scripts/regen-witness.mjs

For external projects, call the plugin script with explicit paths:

node plugins/ruflo-core/scripts/witness/regen.mjs \
  --manifest verification/macos/manifest.md.json \
  --history  verification/macos/history.jsonl \
  --fixes    verification/witness-fixes.json

Output:

witness regen summary
─────────────────────
  gitCommit:    abc123def456…
  branch:       main
  issuedAt:     2026-05-09T00:00:00.000Z
  total fixes:  1  (was 0)
  verified:     1
  missing:      0
  new entries:  MY-001
written:  verification/macos/manifest.md.json
appended: verification/macos/history.jsonl

verified: N/N confirms every marker is present in its cited file.

4. Verify

node plugins/ruflo-core/scripts/witness/verify.mjs \
  --manifest verification/macos/manifest.md.json

Output:

Manifest signature:
  hash matches:                    yes
  public key reproducible:         yes
  Ed25519 signature valid:         yes

Summary: pass=1 drift=0 regressed=0 missing=0

If regressed > 0 or signatureValid: no, the manifest has been tampered with or a documented fix's marker has been deleted.

5. Investigate a regression

When CI reports F12 regressed:

node plugins/ruflo-core/scripts/witness/history.mjs \
  --history verification/macos/history.jsonl regressions

Output:

F12
  last pass:    a1b2c3d4  2026-05-07T14:23:11.000Z
  regressed at: 9f8e7d6c  2026-05-08T09:14:55.000Z

Then git log lastPass..regressedAt -- <file> collapses bisect from "many commits" to "the few in this 18-hour window."

6. Wire into CI

Add to .github/workflows/<your-pipeline>.yml:

witness-verify:
  strategy:
    matrix:
      os: [ubuntu-latest, macos-latest, windows-latest]
  runs-on: ${{ matrix.os }}
  steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-node@v4
      with: { node-version: '22' }
    - run: npm i @noble/ed25519
    - shell: bash
      run: |
        case "$RUNNER_OS" in
          Linux)   OS_DIR=linux ;;
          macOS)   OS_DIR=macos ;;
          Windows) OS_DIR=windows ;;
        esac
        node plugins/ruflo-core/scripts/witness/verify.mjs \
          --manifest "verification/$OS_DIR/manifest.md.json" \
          --json > /tmp/result.json
        node -e "if (!require('/tmp/result.json').ok) process.exit(1)"

Block publish on failure. Every commit on every OS gets attested.


Features

Feature Mechanism What it catches
SHA-256 fingerprint per fix Per-file hash recorded at issuance Any change to the file
Marker substring Distinctive code substring required to be present Refactors that delete the fix
Ed25519 signature Deterministic seed sha256(gitCommit + ':ruflo-witness/v1') Manifest tampering, key-derivation drift
Reproducible public key Anyone with the git commit re-derives the same pubkey No committed private key needed
Per-OS bundles verification/{linux,macos,windows}/ Platform-specific marker drift (CRLF, path separators)
Temporal history (JSONL) One snapshot appended per regen When a regression was introduced
Drift vs regression sha256 changed but marker present → drift; marker missing → regression False alarms suppressed; real regressions flagged
Status timeline per fix history.mjs timeline --id F12 Flapping markers (too brittle) and persistent drift (too unstable)

Daily workflow cheat sheet

# Add a new fix
$EDITOR verification/witness-fixes.json
node scripts/regen-witness.mjs

# Verify the current tree
node plugins/ruflo-core/scripts/witness/verify.mjs \
  --manifest verification/macos/manifest.md.json

# Diff against the previous snapshot
node plugins/ruflo-core/scripts/witness/history.mjs \
  --history verification/macos/history.jsonl summary

# Find when a regression was introduced
node plugins/ruflo-core/scripts/witness/history.mjs \
  --history verification/macos/history.jsonl regressions

# Status timeline for one fix
node plugins/ruflo-core/scripts/witness/history.mjs \
  --history verification/macos/history.jsonl timeline --id F12

Schema

<os>/manifest.md.json

{
  "manifest": {
    "schema": "ruflo-witness/v1",
    "issuedAt": "2026-05-09T00:00:00.000Z",
    "gitCommit": "<full sha>",
    "branch": "main",
    "os": "macos",                              // matches the folder
    "releases": { "ruflo": "3.7.0-alpha.21", "@claude-flow/plugin-agent-federation": "1.0.0-alpha.15" },
    "summary": { "totalFixes": 102, "verified": 102, "missing": 0 },
    "fixes": [
      {
        "id": "F1",
        "desc": "...",
        "file": "v3/@claude-flow/cli/dist/...",
        "sha256": "<64 hex>",
        "marker": "<distinctive substring>",
        "markerVerified": true
      }
    ]
  },
  "integrity": {
    "manifestHashAlgo": "sha256",
    "manifestHash": "<64 hex of canonical manifest>",
    "signature": "<64-byte hex of Ed25519 signature over canonical manifest>",
    "signatureAlgo": "ed25519",
    "publicKey": "<32-byte hex>",
    "signature": "<64-byte hex>",
    "seedDerivation": "sha256(gitCommit + ':ruflo-witness/v1')"
  }
}

<os>/history.jsonl (one entry per line)

{
  "v": 1,
  "commit": "<full sha>",
  "issuedAt": "2026-05-09T00:00:00.000Z",
  "branch": "main",
  "os": "macos",
  "manifestHash": "<hex>",
  "summary": { "totalFixes": 82, "verified": 82, "missing": 0 },
  "fixes": {
    "F1":     { "sha256": "...", "markerVerified": true },
    "#1867":  { "sha256": "...", "markerVerified": true }
  }
}

witness-fixes.json (input, OS-independent)

{
  "fixes": [
    {
      "id": "MY-001",
      "desc": "human-readable description",
      "file": "path/relative/to/repo/root.js",
      "marker": "distinctive substring that must remain in the file"
    }
  ]
}

Anti-patterns

  • Hand-editing manifest.md.json — breaks the signature. Always regenerate via regen.mjs.
  • Markers that match generic patterns ('function', 'import', 'TODO') — false positives or flapping.
  • Skipping the history append — without --history, you lose Layer 3 (regression introduction time).
  • Committing the manifest without the history — they belong in the same commit.
  • Cross-OS manifest editing — the manifest is signed for the OS that generated it. Don't copy a Linux manifest into the macOS folder.

How it integrates with the rest of ruflo's regression stack

Layer Where What it catches
Layer 1 — install smoke v3/@claude-flow/memory/scripts/smoke-no-bsqlite.mjs + CI smoke-install-no-bsqlite npm install failures on platforms without prebuilds
Layer 1 — hook smoke plugins/ruflo-core/scripts/test-hooks.mjs + CI plugin-hooks-smoke Plugin/CLI flag drift, parser ambiguity
Layer 1 — MCP protocol smoke plugins/ruflo-core/scripts/test-mcp-protocol.mjs + CI mcp-protocol-smoke HTTP MCP wire-format compliance
Layer 1 — memory-import smoke plugins/ruflo-core/scripts/test-memory-import.mjs + CI memory-import-smoke Memory_import_claude WSL path + key sanitization regressions
Layer 1 — tool-description audit scripts/audit-tool-descriptions.mjs + CI tool-descriptions-audit (ADR-112) Every MCP tool description must have "Use when … is wrong because …" guidance + length ≥ 80 + unique. Baseline at verification/mcp-tool-baseline.json monotone-decreasing
Layer 2 — witness manifest verification/<os>/manifest.md.json + CI witness-verify Documented fix marker disappearing
Layer 3 — temporal history verification/<os>/history.jsonl + history.mjs When a regression was introduced

All CI jobs gate publish. A regression in any layer blocks the release on the platform where it was caught.


References