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.

tools/registry.py

@@ -117,11 +117,27 @@ class ToolRegistry:
         with self._lock:
             existing = self._tools.get(name)
             if existing and existing.toolset != toolset:
-                logger.warning(
-                    "Tool name collision: '%s' (toolset '%s') is being "
-                    "overwritten by toolset '%s'",
-                    name, existing.toolset, toolset,
+                # Allow MCP-to-MCP overwrites (legitimate: server refresh,
+                # or two MCP servers with overlapping tool names).
+                both_mcp = (
+                    existing.toolset.startswith("mcp-")
+                    and toolset.startswith("mcp-")
                 )
+                if both_mcp:
+                    logger.debug(
+                        "Tool '%s': MCP toolset '%s' overwriting MCP toolset '%s'",
+                        name, toolset, existing.toolset,
+                    )
+                else:
+                    # Reject shadowing — prevent plugins/MCP from overwriting
+                    # built-in tools or vice versa.
+                    logger.error(
+                        "Tool registration REJECTED: '%s' (toolset '%s') would "
+                        "shadow existing tool from toolset '%s'. Deregister the "
+                        "existing tool first if this is intentional.",
+                        name, toolset, existing.toolset,
+                    )
+                    return
             self._tools[name] = ToolEntry(
                 name=name,
                 toolset=toolset,