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/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