fix(mcp): clarify enabledTools filtering semantics

- support both raw and wrapped MCP tool names
- treat [\"*\"] as all tools and [] as no tools
- add warnings, tests, and README docs for enabledTools

README.md

@@ -1112,6 +1112,28 @@ Use `toolTimeout` to override the default 30s per-call timeout for slow servers:
 }
 ```
 
+Use `enabledTools` to register only a subset of tools from an MCP server:
+
+```json
+{
+  "tools": {
+    "mcpServers": {
+      "filesystem": {
+        "command": "npx",
+        "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/dir"],
+        "enabledTools": ["read_file", "mcp_filesystem_write_file"]
+      }
+    }
+  }
+}
+```
+
+`enabledTools` accepts either the raw MCP tool name (for example `read_file`) or the wrapped nanobot tool name (for example `mcp_filesystem_write_file`).
+
+- Omit `enabledTools`, or set it to `["*"]`, to register all tools.
+- Set `enabledTools` to `[]` to register no tools from that server.
+- Set `enabledTools` to a non-empty list of names to register only that subset.
+
 MCP tools are automatically discovered and registered on startup. The LLM can use them alongside built-in tools — no extra configuration needed.
 
 

nanobot/agent/tools/mcp.py

@@ -138,16 +138,46 @@ async def connect_mcp_servers(
             await session.initialize()
 
             tools = await session.list_tools()
-            enabled_tools = set(cfg.enabled_tools) if cfg.enabled_tools else None
+            enabled_tools = set(cfg.enabled_tools)
+            allow_all_tools = "*" in enabled_tools
             registered_count = 0
+            matched_enabled_tools: set[str] = set()
+            available_raw_names = [tool_def.name for tool_def in tools.tools]
+            available_wrapped_names = [f"mcp_{name}_{tool_def.name}" for tool_def in tools.tools]
             for tool_def in tools.tools:
-                if enabled_tools and tool_def.name not in enabled_tools:
+                wrapped_name = f"mcp_{name}_{tool_def.name}"
-                    logger.debug("MCP: skipping tool '{}' from server '{}' (not in enabledTools)", tool_def.name, name)
+                if (
+                    not allow_all_tools
+                    and tool_def.name not in enabled_tools
+                    and wrapped_name not in enabled_tools
+                ):
+                    logger.debug(
+                        "MCP: skipping tool '{}' from server '{}' (not in enabledTools)",
+                        wrapped_name,
+                        name,
+                    )
                     continue
                 wrapper = MCPToolWrapper(session, name, tool_def, tool_timeout=cfg.tool_timeout)
                 registry.register(wrapper)
                 logger.debug("MCP: registered tool '{}' from server '{}'", wrapper.name, name)
                 registered_count += 1
+                if enabled_tools:
+                    if tool_def.name in enabled_tools:
+                        matched_enabled_tools.add(tool_def.name)
+                    if wrapped_name in enabled_tools:
+                        matched_enabled_tools.add(wrapped_name)
+
+            if enabled_tools and not allow_all_tools:
+                unmatched_enabled_tools = sorted(enabled_tools - matched_enabled_tools)
+                if unmatched_enabled_tools:
+                    logger.warning(
+                        "MCP server '{}': enabledTools entries not found: {}. Available raw names: {}. "
+                        "Available wrapped names: {}",
+                        name,
+                        ", ".join(unmatched_enabled_tools),
+                        ", ".join(available_raw_names) or "(none)",
+                        ", ".join(available_wrapped_names) or "(none)",
+                    )
 
             logger.info("MCP server '{}': connected, {} tools registered", name, registered_count)
         except Exception as e:

nanobot/config/schema.py

@@ -140,7 +140,7 @@ class MCPServerConfig(Base):
     url: str = ""  # HTTP/SSE: endpoint URL
     headers: dict[str, str] = Field(default_factory=dict)  # HTTP/SSE: custom headers
     tool_timeout: int = 30  # seconds before a tool call is cancelled
-    enabled_tools: list[str] = Field(default_factory=list)  # Only register these tools; empty = all tools
+    enabled_tools: list[str] = Field(default_factory=lambda: ["*"])  # Only register these tools; accepts raw MCP names or wrapped mcp_<server>_<tool> names; ["*"] = all tools; [] = no tools
 
 class ToolsConfig(Base):
     """Tools configuration."""

tests/test_mcp_tool.py

@@ -1,12 +1,15 @@
 from __future__ import annotations
 
 import asyncio
+from contextlib import AsyncExitStack, asynccontextmanager
 import sys
 from types import ModuleType, SimpleNamespace
 
 import pytest
 
-from nanobot.agent.tools.mcp import MCPToolWrapper
+from nanobot.agent.tools.mcp import MCPToolWrapper, connect_mcp_servers
+from nanobot.agent.tools.registry import ToolRegistry
+from nanobot.config.schema import MCPServerConfig
 
 
 class _FakeTextContent:
@@ -14,12 +17,63 @@ class _FakeTextContent:
         self.text = text
 
 
+@pytest.fixture
+def fake_mcp_runtime() -> dict[str, object | None]:
+    return {"session": None}
+
+
 @pytest.fixture(autouse=True)
-def _fake_mcp_module(monkeypatch: pytest.MonkeyPatch) -> None:
+def _fake_mcp_module(
+    monkeypatch: pytest.MonkeyPatch, fake_mcp_runtime: dict[str, object | None]
+) -> None:
     mod = ModuleType("mcp")
     mod.types = SimpleNamespace(TextContent=_FakeTextContent)
+
+    class _FakeStdioServerParameters:
+        def __init__(self, command: str, args: list[str], env: dict | None = None) -> None:
+            self.command = command
+            self.args = args
+            self.env = env
+
+    class _FakeClientSession:
+        def __init__(self, _read: object, _write: object) -> None:
+            self._session = fake_mcp_runtime["session"]
+
+        async def __aenter__(self) -> object:
+            return self._session
+
+        async def __aexit__(self, exc_type, exc, tb) -> bool:
+            return False
+
+    @asynccontextmanager
+    async def _fake_stdio_client(_params: object):
+        yield object(), object()
+
+    @asynccontextmanager
+    async def _fake_sse_client(_url: str, httpx_client_factory=None):
+        yield object(), object()
+
+    @asynccontextmanager
+    async def _fake_streamable_http_client(_url: str, http_client=None):
+        yield object(), object(), object()
+
+    mod.ClientSession = _FakeClientSession
+    mod.StdioServerParameters = _FakeStdioServerParameters
     monkeypatch.setitem(sys.modules, "mcp", mod)
 
+    client_mod = ModuleType("mcp.client")
+    stdio_mod = ModuleType("mcp.client.stdio")
+    stdio_mod.stdio_client = _fake_stdio_client
+    sse_mod = ModuleType("mcp.client.sse")
+    sse_mod.sse_client = _fake_sse_client
+    streamable_http_mod = ModuleType("mcp.client.streamable_http")
+    streamable_http_mod.streamable_http_client = _fake_streamable_http_client
+
+    monkeypatch.setitem(sys.modules, "mcp.client", client_mod)
+    monkeypatch.setitem(sys.modules, "mcp.client.stdio", stdio_mod)
+    monkeypatch.setitem(sys.modules, "mcp.client.sse", sse_mod)
+    monkeypatch.setitem(sys.modules, "mcp.client.streamable_http", streamable_http_mod)
+
 
 def _make_wrapper(session: object, *, timeout: float = 0.1) -> MCPToolWrapper:
     tool_def = SimpleNamespace(
@@ -97,3 +151,132 @@ async def test_execute_handles_generic_exception() -> None:
     result = await wrapper.execute()
 
     assert result == "(MCP tool call failed: RuntimeError)"
+
+
+def _make_tool_def(name: str) -> SimpleNamespace:
+    return SimpleNamespace(
+        name=name,
+        description=f"{name} tool",
+        inputSchema={"type": "object", "properties": {}},
+    )
+
+
+def _make_fake_session(tool_names: list[str]) -> SimpleNamespace:
+    async def initialize() -> None:
+        return None
+
+    async def list_tools() -> SimpleNamespace:
+        return SimpleNamespace(tools=[_make_tool_def(name) for name in tool_names])
+
+    return SimpleNamespace(initialize=initialize, list_tools=list_tools)
+
+
+@pytest.mark.asyncio
+async def test_connect_mcp_servers_enabled_tools_supports_raw_names(
+    fake_mcp_runtime: dict[str, object | None],
+) -> None:
+    fake_mcp_runtime["session"] = _make_fake_session(["demo", "other"])
+    registry = ToolRegistry()
+    stack = AsyncExitStack()
+    await stack.__aenter__()
+    try:
+        await connect_mcp_servers(
+            {"test": MCPServerConfig(command="fake", enabled_tools=["demo"])},
+            registry,
+            stack,
+        )
+    finally:
+        await stack.aclose()
+
+    assert registry.tool_names == ["mcp_test_demo"]
+
+
+@pytest.mark.asyncio
+async def test_connect_mcp_servers_enabled_tools_defaults_to_all(
+    fake_mcp_runtime: dict[str, object | None],
+) -> None:
+    fake_mcp_runtime["session"] = _make_fake_session(["demo", "other"])
+    registry = ToolRegistry()
+    stack = AsyncExitStack()
+    await stack.__aenter__()
+    try:
+        await connect_mcp_servers(
+            {"test": MCPServerConfig(command="fake")},
+            registry,
+            stack,
+        )
+    finally:
+        await stack.aclose()
+
+    assert registry.tool_names == ["mcp_test_demo", "mcp_test_other"]
+
+
+@pytest.mark.asyncio
+async def test_connect_mcp_servers_enabled_tools_supports_wrapped_names(
+    fake_mcp_runtime: dict[str, object | None],
+) -> None:
+    fake_mcp_runtime["session"] = _make_fake_session(["demo", "other"])
+    registry = ToolRegistry()
+    stack = AsyncExitStack()
+    await stack.__aenter__()
+    try:
+        await connect_mcp_servers(
+            {"test": MCPServerConfig(command="fake", enabled_tools=["mcp_test_demo"])},
+            registry,
+            stack,
+        )
+    finally:
+        await stack.aclose()
+
+    assert registry.tool_names == ["mcp_test_demo"]
+
+
+@pytest.mark.asyncio
+async def test_connect_mcp_servers_enabled_tools_empty_list_registers_none(
+    fake_mcp_runtime: dict[str, object | None],
+) -> None:
+    fake_mcp_runtime["session"] = _make_fake_session(["demo", "other"])
+    registry = ToolRegistry()
+    stack = AsyncExitStack()
+    await stack.__aenter__()
+    try:
+        await connect_mcp_servers(
+            {"test": MCPServerConfig(command="fake", enabled_tools=[])},
+            registry,
+            stack,
+        )
+    finally:
+        await stack.aclose()
+
+    assert registry.tool_names == []
+
+
+@pytest.mark.asyncio
+async def test_connect_mcp_servers_enabled_tools_warns_on_unknown_entries(
+    fake_mcp_runtime: dict[str, object | None], monkeypatch: pytest.MonkeyPatch
+) -> None:
+    fake_mcp_runtime["session"] = _make_fake_session(["demo"])
+    registry = ToolRegistry()
+    warnings: list[str] = []
+
+    def _warning(message: str, *args: object) -> None:
+        warnings.append(message.format(*args))
+
+    monkeypatch.setattr("nanobot.agent.tools.mcp.logger.warning", _warning)
+
+    stack = AsyncExitStack()
+    await stack.__aenter__()
+    try:
+        await connect_mcp_servers(
+            {"test": MCPServerConfig(command="fake", enabled_tools=["unknown"])},
+            registry,
+            stack,
+        )
+    finally:
+        await stack.aclose()
+
+    assert registry.tool_names == []
+    assert warnings
+    assert "enabledTools entries not found: unknown" in warnings[-1]
+    assert "Available raw names: demo" in warnings[-1]
+    assert "Available wrapped names: mcp_test_demo" in warnings[-1]