security: supply chain hardening — CI pinning, dep pinning, and code fixes (#9801)

CI/CD Hardening:
- Pin all 12 GitHub Actions to full commit SHAs (was mutable @vN tags)
- Add explicit permissions: {contents: read} to 4 workflows
- Pin CI pip installs to exact versions (pyyaml==6.0.2, httpx==0.28.1)
- Extend supply-chain-audit.yml to scan workflow, Dockerfile, dependency
  manifest, and Actions version changes

Dependency Pinning:
- Pin git-based Python deps to commit SHAs (atroposlib, tinker, yc-bench)
- Pin WhatsApp Baileys from mutable branch to commit SHA

Tool Registry:
- Reject tool name shadowing from different tool families (plugins/MCP
  cannot overwrite built-in tools). MCP-to-MCP overwrites still allowed.

MCP Security:
- Add tool description content scanning for prompt injection patterns
- Log detailed change diff on dynamic tool refresh at WARNING level

Skill Manager:
- Fix dangerous verdict bug: agent-created skills with dangerous
  findings were silently allowed (ask->None->allow). Now blocked.

.github/workflows/contributor-check.yml

@@ -9,11 +9,14 @@ on:
       - '**/*.py'
       - '.github/workflows/contributor-check.yml'
 
+permissions:
+  contents: read
+
 jobs:
   check-attribution:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
         with:
           fetch-depth: 0  # Full history needed for git log
 

.github/workflows/deploy-site.yml

@@ -28,20 +28,20 @@ jobs:
       name: github-pages
       url: ${{ steps.deploy.outputs.page_url }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020  # v4
         with:
           node-version: 20
           cache: npm
           cache-dependency-path: website/package-lock.json
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5
         with:
           python-version: '3.11'
 
       - name: Install PyYAML for skill extraction
-        run: pip install pyyaml httpx
+        run: pip install pyyaml==6.0.2 httpx==0.28.1
 
       - name: Extract skill metadata for dashboard
         run: python3 website/scripts/extract-skills.py
@@ -73,10 +73,10 @@ jobs:
           echo "hermes-agent.nousresearch.com" > _site/CNAME
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa  # v3
         with:
           path: _site
 
       - name: Deploy to GitHub Pages
         id: deploy
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e  # v4

.github/workflows/docker-publish.yml

@@ -23,21 +23,21 @@ jobs:
     timeout-minutes: 60
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
         with:
           submodules: recursive
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130  # v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f  # v3
 
       # Build amd64 only so we can `load` the image for smoke testing.
       # `load: true` cannot export a multi-arch manifest to the local daemon.
       # The multi-arch build follows on push to main / release.
       - name: Build image (amd64, smoke test)
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8  # v6
         with:
           context: .
           file: Dockerfile
@@ -56,14 +56,14 @@ jobs:
 
       - name: Log in to Docker Hub
         if: github.event_name == 'push' && github.ref == 'refs/heads/main' || github.event_name == 'release'
-        uses: docker/login-action@v3
+        uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9  # v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Push multi-arch image (main branch)
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8  # v6
         with:
           context: .
           file: Dockerfile
@@ -75,7 +75,7 @@ jobs:
 
       - name: Push multi-arch image (release)
         if: github.event_name == 'release'
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8  # v6
         with:
           context: .
           file: Dockerfile

.github/workflows/docs-site-checks.yml

@@ -7,13 +7,16 @@ on:
       - '.github/workflows/docs-site-checks.yml'
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   docs-site-checks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020  # v4
         with:
           node-version: 20
           cache: npm
@@ -23,7 +26,7 @@ jobs:
         run: npm ci
         working-directory: website
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5
         with:
           python-version: '3.11'
 

.github/workflows/nix.yml

@@ -14,6 +14,9 @@ on:
       - 'run_agent.py'
       - 'acp_adapter/**'
 
+permissions:
+  contents: read
+
 concurrency:
   group: nix-${{ github.ref }}
   cancel-in-progress: true
@@ -26,7 +29,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: DeterminateSystems/nix-installer-action@ef8a148080ab6020fd15196c2084a2eea5ff2d25  # v22
       - uses: DeterminateSystems/magic-nix-cache-action@565684385bcd71bad329742eefe8d12f2e765b39  # v13
       - name: Check flake

.github/workflows/skills-index.yml

@@ -20,14 +20,14 @@ jobs:
     if: github.repository == 'NousResearch/hermes-agent'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5
         with:
           python-version: '3.11'
 
       - name: Install dependencies
-        run: pip install httpx pyyaml
+        run: pip install httpx==0.28.1 pyyaml==6.0.2
 
       - name: Build skills index
         env:
@@ -35,7 +35,7 @@ jobs:
         run: python scripts/build_skills_index.py
 
       - name: Upload index artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02  # v4
         with:
           name: skills-index
           path: website/static/api/skills-index.json
@@ -53,25 +53,25 @@ jobs:
     # Only deploy on schedule or manual trigger (not on every push to the script)
     if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093  # v4
         with:
           name: skills-index
           path: website/static/api/
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020  # v4
         with:
           node-version: 20
           cache: npm
           cache-dependency-path: website/package-lock.json
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065  # v5
         with:
           python-version: '3.11'
 
       - name: Install PyYAML for skill extraction
-        run: pip install pyyaml
+        run: pip install pyyaml==6.0.2
 
       - name: Extract skill metadata for dashboard
         run: python3 website/scripts/extract-skills.py
@@ -92,10 +92,10 @@ jobs:
           echo "hermes-agent.nousresearch.com" > _site/CNAME
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa  # v3
         with:
           path: _site
 
       - name: Deploy to GitHub Pages
         id: deploy
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e  # v4

.github/workflows/supply-chain-audit.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
         with:
           fetch-depth: 0
 
@@ -149,6 +149,62 @@ jobs:
           "
           fi
 
+          # --- CI/CD workflow files modified ---
+          WORKFLOW_HITS=$(git diff --name-only "$BASE".."$HEAD" | grep -E '\.github/workflows/.*\.ya?ml$' || true)
+          if [ -n "$WORKFLOW_HITS" ]; then
+            FINDINGS="${FINDINGS}
+          ### ⚠️ WARNING: CI/CD workflow files modified
+          Changes to workflow files can alter build pipelines, inject steps, or modify permissions. Verify no unauthorized actions or secrets access were added.
+
+          **Files:**
+          \`\`\`
+          ${WORKFLOW_HITS}
+          \`\`\`
+          "
+          fi
+
+          # --- Dockerfile / container build files modified ---
+          DOCKER_HITS=$(git diff --name-only "$BASE".."$HEAD" | grep -iE '(Dockerfile|\.dockerignore|docker-compose)' || true)
+          if [ -n "$DOCKER_HITS" ]; then
+            FINDINGS="${FINDINGS}
+          ### ⚠️ WARNING: Container build files modified
+          Changes to Dockerfiles or compose files can alter base images, add build steps, or expose ports. Verify base image pins and build commands.
+
+          **Files:**
+          \`\`\`
+          ${DOCKER_HITS}
+          \`\`\`
+          "
+          fi
+
+          # --- Dependency manifest files modified ---
+          DEP_HITS=$(git diff --name-only "$BASE".."$HEAD" | grep -E '(pyproject\.toml|requirements.*\.txt|package\.json|Gemfile|go\.mod|Cargo\.toml)$' || true)
+          if [ -n "$DEP_HITS" ]; then
+            FINDINGS="${FINDINGS}
+          ### ⚠️ WARNING: Dependency manifest files modified
+          Changes to dependency files can introduce new packages or change version pins. Verify all dependency changes are intentional and from trusted sources.
+
+          **Files:**
+          \`\`\`
+          ${DEP_HITS}
+          \`\`\`
+          "
+          fi
+
+          # --- GitHub Actions version unpinning (mutable tags instead of SHAs) ---
+          ACTIONS_UNPIN=$(echo "$DIFF" | grep -n '^\+' | grep 'uses:' | grep -v '#' | grep -E '@v[0-9]' | head -10 || true)
+          if [ -n "$ACTIONS_UNPIN" ]; then
+            FINDINGS="${FINDINGS}
+          ### ⚠️ WARNING: GitHub Actions with mutable version tags
+          Actions should be pinned to full commit SHAs (not \`@v4\`, \`@v5\`). Mutable tags can be retargeted silently if a maintainer account is compromised.
+
+          **Matches:**
+          \`\`\`
+          ${ACTIONS_UNPIN}
+          \`\`\`
+          "
+          fi
+
           # --- Output results ---
           if [ -n "$FINDINGS" ]; then
             echo "found=true" >> "$GITHUB_OUTPUT"

.github/workflows/tests.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [main]
 
+permissions:
+  contents: read
+
 # Cancel in-progress runs for the same PR/branch
 concurrency:
   group: tests-${{ github.ref }}
@@ -17,13 +20,13 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
       - name: Install system dependencies
         run: sudo apt-get update && sudo apt-get install -y ripgrep
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86  # v5
 
       - name: Set up Python 3.11
         run: uv python install 3.11
@@ -49,10 +52,10 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86  # v5
 
       - name: Set up Python 3.11
         run: uv python install 3.11