refactor: remove agent-callable send_message tool (#47856)

* feat(mcp): raise default tool-call timeout 120s -> 300s

Port from openai/codex#28234. Long-running MCP tools (web fetches,
sandboxed builds, deep-research servers) routinely exceed 120s, causing
spurious timeout failures. Codex bumped its default MCP tool timeout from
120 to 300 for the same reason.

- _DEFAULT_TOOL_TIMEOUT 120 -> 300 in tools/mcp_tool.py (per-server
  'timeout' config override unchanged)
- update test_default_timeout assertion
- document the default in mcp-config-reference.md

* refactor: remove agent-callable send_message tool

The agent should not decide on its own to fire off cross-platform
messages or reactions. Outbound platform messaging is handled outside
the agent loop — cron delivery, the gateway kanban notifier
(dashboard-toggled), and the `hermes send` CLI.

Removes the model-tool registration only; the send engine in
send_message_tool.py (_send_to_platform, _send_via_adapter,
_parse_target_ref, per-platform _send_* helpers) is kept intact for
those non-agent callers. Drops the now-empty 'messaging' toolset and
its `hermes tools` toggle. Yuanbao DM guidance now points at the
native yb_send_dm tool.

tests/tools/test_mcp_tool.py

@@ -1884,7 +1884,7 @@ class TestConfigurableTimeouts:
 
         server = MCPServerTask("test_srv")
         assert server.tool_timeout == _DEFAULT_TOOL_TIMEOUT
-        assert server.tool_timeout == 120
+        assert server.tool_timeout == 300
 
     def test_custom_timeout(self):
         """Server with timeout=180 in config gets 180."""