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/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'