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.

scripts/whatsapp-bridge/package.json

@@ -8,7 +8,7 @@
     "start": "node bridge.js"
   },
   "dependencies": {
-    "@whiskeysockets/baileys": "WhiskeySockets/Baileys#fix/abprops-abt-fetch",
+    "@whiskeysockets/baileys": "WhiskeySockets/Baileys#01047debd81beb20da7b7779b08edcb06aa03770",
     "express": "^4.21.0",
     "qrcode-terminal": "^0.12.0",
     "pino": "^9.0.0"