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/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