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/tests.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [main]
 
+permissions:
+  contents: read
+
 # Cancel in-progress runs for the same PR/branch
 concurrency:
   group: tests-${{ github.ref }}
@@ -17,13 +20,13 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
       - name: Install system dependencies
         run: sudo apt-get update && sudo apt-get install -y ripgrep
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86  # v5
 
       - name: Set up Python 3.11
         run: uv python install 3.11
@@ -49,10 +52,10 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86  # v5
 
       - name: Set up Python 3.11
         run: uv python install 3.11