fix(runtime): resolve Wave 3-S audit findings (P2-1, P2-2, P2-3)

- P2-1: reject non-process PID values (None, 0, negative integers) in pid_alive
  without invoking underlying process probe.
- P2-2: truthfully represent production external bridge executions as uncontained,
  external, non-authoritative grants carrying sanitized endpoint metadata.
- P2-3: reject writable_extra overlay bindings over protected system roots and
  their descendants while preserving legitimate scratch destinations.

src/agent_tools/subprocess_tools.py

@@ -653,6 +653,16 @@ class HostShellTool:
             requested_timeout = 30
         timeout = max(1, min(requested_timeout, 120))
 
+        from src import containment
+        from src.tool_execution import agent_cwd
+
+        sanitized_endpoint = f"{parsed.scheme}://{parsed.netloc}{parsed.path}" if parsed.scheme and parsed.netloc else "host_shell_bridge"
+        owner = str(ctx.get("session_id") or ctx.get("owner") or "host_shell")
+        spec = _owned_spec(agent_cwd(), ctx.get("subproc_env"), timeout)
+        grant = containment.declare_external_bridge(spec, owner=owner, endpoint=sanitized_endpoint)
+        boundary = grant.to_dict()
+        boundary["executed"] = False
+
         request_body: dict[str, object] = {"timeout": timeout}
         request_id = ""
         if job_id:
@@ -676,6 +686,8 @@ class HostShellTool:
                     return {
                         "error": f"host_shell: bridge returned HTTP {resp.status_code}",
                         "exit_code": 1,
+                        "host_bridge": "tui",
+                        "containment": boundary,
                     }
                 data = resp.json()
 
@@ -702,6 +714,8 @@ class HostShellTool:
                             return {
                                 "error": f"host_shell: bridge returned HTTP {poll.status_code}",
                                 "exit_code": 1,
+                                "host_bridge": "tui",
+                                "containment": boundary,
                             }
                         data = poll.json()
                         if not isinstance(data, dict):
@@ -732,15 +746,16 @@ class HostShellTool:
                 task.add_done_callback(_HOST_SHELL_CANCEL_TASKS.discard)
             raise
         except Exception as e:
-            return {"error": f"host_shell: bridge call failed: {e}", "exit_code": 1}
+            return {"error": f"host_shell: bridge call failed: {e}", "exit_code": 1, "containment": boundary}
 
         if not isinstance(data, dict):
-            return {"error": "host_shell: bridge returned invalid payload", "exit_code": 1}
+            return {"error": "host_shell: bridge returned invalid payload", "exit_code": 1, "containment": boundary}
         if data.get("error"):
             return {
                 "error": _truncate(str(data["error"]), MAX_OUTPUT_CHARS),
                 "exit_code": 1,
                 "host_bridge": "tui",
+                "containment": boundary,
             }
         stdout = str(data.get("stdout") or data.get("output") or "")
         stderr = str(data.get("stderr") or "")
@@ -754,15 +769,18 @@ class HostShellTool:
                 "error": "host_shell: bridge returned an invalid exit_code",
                 "exit_code": 1,
                 "host_bridge": "tui",
+                "containment": boundary,
             }
         exit_code = raw_exit_code
         output = stdout.rstrip()
         if stderr.strip():
             output = (output + "\nSTDERR: " + stderr.strip()).strip() if output else "STDERR: " + stderr.strip()
+        boundary["executed"] = True
         result = {
             "output": _truncate(output, MAX_OUTPUT_CHARS) or "(no output)",
             "exit_code": exit_code,
             "host_bridge": "tui",
+            "containment": boundary,
         }
         for key in ("detached", "job_id", "status", "running", "finished", "cwd"):
             if key in data:

src/containment.py

@@ -121,9 +121,35 @@ _DEATH_POLL_S = 0.05
 # private /tmp or the workspace itself with a host directory would undo the
 # namespace from inside the argv that builds it.
 _RESERVED_BIND_DESTS = frozenset({
-    "/", "/tmp", "/proc", "/dev", "/sys", WORKSPACE_MOUNT,
+    "/", "/tmp", "/home", "/proc", "/dev", "/sys", WORKSPACE_MOUNT,
 })
 
+# System hierarchies where a writable overlay would invalidate the boundary
+# established by bubblewrap. Reject both exact roots and all descendants.
+_PROTECTED_WRITABLE_HIERARCHIES = frozenset({
+    "/etc",
+    "/usr",
+    "/bin",
+    "/sbin",
+    "/lib",
+    "/lib64",
+    "/proc",
+    "/dev",
+    "/sys",
+    "/root",
+    WORKSPACE_MOUNT,
+})
+
+
+def _is_protected_writable_destination(path: str) -> bool:
+    normalized = os.path.abspath(path)
+    if normalized in _RESERVED_BIND_DESTS:
+        return True
+    for root in _PROTECTED_WRITABLE_HIERARCHIES:
+        if normalized == root or normalized.startswith(root.rstrip(os.sep) + os.sep):
+            return True
+    return False
+
 # WORKSPACE_MOUNT is re-exported from src.constants: where the workspace is
 # mounted inside a namespace is a property of the tool contract, not of this
 # module, and two definitions of it would be two contracts.
@@ -217,6 +243,7 @@ class ContainmentGrant:
     pgid: Optional[int] = None
     namespace_pid: Optional[int] = None
     namespace_start_token: Optional[str] = None
+    endpoint: Optional[str] = None
 
     @property
     def contained(self) -> bool:
@@ -229,7 +256,7 @@ class ContainmentGrant:
         Deliberately omits ``env``: it is part of the boundary but it is also
         where credentials live, and a tool result is model-visible.
         """
-        return {
+        data = {
             "id": self.id,
             "mechanism": self.mechanism,
             "mode": self.mode,
@@ -242,6 +269,9 @@ class ContainmentGrant:
             "requested": sorted(self.spec.requested),
             "network": self.spec.network,
         }
+        if self.endpoint:
+            data["endpoint"] = self.endpoint
+        return data
 
 
 @dataclass(frozen=True)
@@ -480,6 +510,7 @@ def _write_record(grant: ContainmentGrant) -> None:
         "pgid": grant.pgid,
         "namespace_pid": grant.namespace_pid,
         "namespace_start_token": grant.namespace_start_token,
+        "endpoint": grant.endpoint,
         "acquired_at": time.time(),
         "released_at": None,
         "release": None,
@@ -581,6 +612,9 @@ def _validate_spec(spec: ContainmentSpec) -> ContainmentSpec:
     for path in writable + readonly:
         if path in _RESERVED_BIND_DESTS:
             raise ValueError(f"containment: refusing to bind over reserved path {path}")
+    for path in writable:
+        if _is_protected_writable_destination(path):
+            raise ValueError(f"containment: refusing to bind over reserved path {path}")
     return replace(spec, workspace=workspace, writable_extra=writable, readonly_extra=readonly)
 
 
@@ -770,6 +804,7 @@ def declare_external_bridge(
         mode=CONTAINMENT_MODE,
         spec=spec,
         external=True,
+        endpoint=endpoint,
     )
     logger.info(
         "containment: grant %s is external (%s); nothing local contains it",

src/tool_execution.py

@@ -348,9 +348,24 @@ def _text_write_to_binary_artifact_result(content: str) -> tuple[str, Dict] | No
 
 async def _route_tool_via_bridge(tool: str, content: str, session_id: Optional[str], client_runtime_context: Optional[Dict]):
     import base64
+    from urllib.parse import urlparse
     bridge = _client_bridge(client_runtime_context)
     if bridge is None:
         return tool, {"error": f"{tool}: TUI host bridge is not available", "exit_code": 1}
+
+    url = str(bridge.get("url") or "").strip()
+    parsed = urlparse(url)
+    sanitized_endpoint = f"{parsed.scheme}://{parsed.netloc}{parsed.path}" if parsed.scheme and parsed.netloc else "tui_bridge"
+    from src import containment
+    spec = containment.agent_spec(agent_cwd(), {}, int(_BRIDGE_TOOL_TIMEOUT_S))
+    grant = containment.declare_external_bridge(
+        spec,
+        owner=str(session_id or "tui_bridge"),
+        endpoint=sanitized_endpoint,
+    )
+    boundary = grant.to_dict()
+    boundary["executed"] = False
+
     if tool == "bash":
         from src.agent_tools.subprocess_tools import _host_shell_requires_detach, _host_shell_should_auto_poll
 
@@ -401,9 +416,13 @@ async def _route_tool_via_bridge(tool: str, content: str, session_id: Optional[s
                     "output": "host job still running; poll the returned job_id",
                     "exit_code": 0,
                 }
+        if isinstance(result, dict):
+            b = dict(boundary)
+            b["executed"] = (result.get("exit_code") == 0 or (isinstance(result.get("exit_code"), int) and not result.get("error")))
+            result["containment"] = b
         return desc, result
     if tool == "python":
-        return "python: (client)", await _bridge_post(
+        py_res = await _bridge_post(
             bridge,
             "/run",
             {
@@ -414,6 +433,11 @@ async def _route_tool_via_bridge(tool: str, content: str, session_id: Optional[s
             timeout_s=_BRIDGE_TOOL_TIMEOUT_S,
             err_prefix="python",
         )
+        if isinstance(py_res, dict):
+            b = dict(boundary)
+            b["executed"] = (py_res.get("exit_code") == 0 or (isinstance(py_res.get("exit_code"), int) and not py_res.get("error")))
+            py_res["containment"] = b
+        return "python: (client)", py_res
     if tool == "grep":
         stripped = content.strip()
         try: