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/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"