fix: MCP toolset resolution for runtime and config (#3252)

Gateway sessions had their own inline toolset resolution that only read
platform_toolsets from config, which never includes MCP server names.
MCP tools were discovered and registered but invisible to the model.

- Replace duplicated gateway toolset resolution in _run_agent() and
  _run_background_task() with calls to the shared _get_platform_tools()
- Extend _get_platform_tools() to include globally enabled MCP servers
  at runtime (include_default_mcp_servers=True), while config-editing
  flows use include_default_mcp_servers=False to avoid persisting
  implicit MCP defaults into platform_toolsets
- Add homeassistant to PLATFORMS dict (was missing, caused KeyError)
- Fix CLI entry point to use _get_platform_tools() as well, so MCP
  tools are visible in CLI mode too
- Remove redundant platform_key reassignment in _run_background_task

Co-authored-by: kshitijk4poor <kshitijk4poor@users.noreply.github.com>

cli.py

@@ -7288,12 +7288,9 @@ def main(
                 else:
                     toolsets_list.append(str(t))
     else:
-        # Check config for CLI toolsets, fallback to hermes-cli
-        config_cli_toolsets = CLI_CONFIG.get("platform_toolsets", {}).get("cli")
-        if config_cli_toolsets and isinstance(config_cli_toolsets, list):
-            toolsets_list = config_cli_toolsets
-        else:
-            toolsets_list = ["hermes-cli"]
+        # Use the shared resolver so MCP servers are included at runtime
+        from hermes_cli.tools_config import _get_platform_tools
+        toolsets_list = sorted(_get_platform_tools(CLI_CONFIG, "cli"))
     
     parsed_skills = _parse_skills_argument(skills)
 

gateway/run.py

@@ -257,7 +257,25 @@ def _resolve_runtime_agent_kwargs() -> dict:
     }
 
 
-def _resolve_gateway_model() -> str:
+def _platform_config_key(platform: "Platform") -> str:
+    """Map a Platform enum to its config.yaml key (LOCAL→"cli", rest→enum value)."""
+    return "cli" if platform == Platform.LOCAL else platform.value
+
+
+def _load_gateway_config() -> dict:
+    """Load and parse ~/.hermes/config.yaml, returning {} on any error."""
+    try:
+        config_path = _hermes_home / 'config.yaml'
+        if config_path.exists():
+            import yaml
+            with open(config_path, 'r', encoding='utf-8') as f:
+                return yaml.safe_load(f) or {}
+    except Exception:
+        logger.debug("Could not load gateway config from %s", _hermes_home / 'config.yaml')
+    return {}
+
+
+def _resolve_gateway_model(config: dict | None = None) -> str:
     """Read model from env/config — mirrors the resolution in _run_agent_sync.
 
     Without this, temporary AIAgent instances (memory flush, /compress) fall
@@ -265,19 +283,12 @@ def _resolve_gateway_model() -> str:
     when the active provider is openai-codex.
     """
     model = os.getenv("HERMES_MODEL") or os.getenv("LLM_MODEL") or "anthropic/claude-opus-4.6"
-    try:
-        import yaml as _y
-        _cfg_path = _hermes_home / "config.yaml"
-        if _cfg_path.exists():
-            with open(_cfg_path, encoding="utf-8") as _f:
-                _cfg = _y.safe_load(_f) or {}
-            _model_cfg = _cfg.get("model", {})
-            if isinstance(_model_cfg, str):
-                model = _model_cfg
-            elif isinstance(_model_cfg, dict):
-                model = _model_cfg.get("default", model)
-    except Exception:
-        pass
+    cfg = config if config is not None else _load_gateway_config()
+    model_cfg = cfg.get("model", {})
+    if isinstance(model_cfg, str):
+        model = model_cfg
+    elif isinstance(model_cfg, dict):
+        model = model_cfg.get("default", model)
     return model
 
 
@@ -3571,52 +3582,12 @@ class GatewayRunner:
                 )
                 return
 
-            # Read model from config via shared helper
-            model = _resolve_gateway_model()
+            user_config = _load_gateway_config()
+            model = _resolve_gateway_model(user_config)
+            platform_key = _platform_config_key(source.platform)
 
-            # Determine toolset (same logic as _run_agent)
-            default_toolset_map = {
-                Platform.LOCAL: "hermes-cli",
-                Platform.TELEGRAM: "hermes-telegram",
-                Platform.DISCORD: "hermes-discord",
-                Platform.WHATSAPP: "hermes-whatsapp",
-                Platform.SLACK: "hermes-slack",
-                Platform.SIGNAL: "hermes-signal",
-                Platform.HOMEASSISTANT: "hermes-homeassistant",
-                Platform.EMAIL: "hermes-email",
-                Platform.DINGTALK: "hermes-dingtalk",
-            }
-            platform_toolsets_config = {}
-            try:
-                config_path = _hermes_home / 'config.yaml'
-                if config_path.exists():
-                    import yaml
-                    with open(config_path, 'r', encoding="utf-8") as f:
-                        user_config = yaml.safe_load(f) or {}
-                    platform_toolsets_config = user_config.get("platform_toolsets", {})
-            except Exception:
-                pass
-
-            platform_config_key = {
-                Platform.LOCAL: "cli",
-                Platform.TELEGRAM: "telegram",
-                Platform.DISCORD: "discord",
-                Platform.WHATSAPP: "whatsapp",
-                Platform.SLACK: "slack",
-                Platform.SIGNAL: "signal",
-                Platform.HOMEASSISTANT: "homeassistant",
-                Platform.EMAIL: "email",
-                Platform.DINGTALK: "dingtalk",
-            }.get(source.platform, "telegram")
-
-            config_toolsets = platform_toolsets_config.get(platform_config_key)
-            if config_toolsets and isinstance(config_toolsets, list):
-                enabled_toolsets = config_toolsets
-            else:
-                default_toolset = default_toolset_map.get(source.platform, "hermes-telegram")
-                enabled_toolsets = [default_toolset]
-
-            platform_key = "cli" if source.platform == Platform.LOCAL else source.platform.value
+            from hermes_cli.tools_config import _get_platform_tools
+            enabled_toolsets = sorted(_get_platform_tools(user_config, platform_key))
 
             pr = self._provider_routing
             max_iterations = int(os.getenv("HERMES_MAX_ITERATIONS", "90"))
@@ -4742,67 +4713,16 @@ class GatewayRunner:
         from run_agent import AIAgent
         import queue
         
-        # Determine toolset based on platform.
-        # Check config.yaml for per-platform overrides, fallback to hardcoded defaults.
-        default_toolset_map = {
-            Platform.LOCAL: "hermes-cli",
-            Platform.TELEGRAM: "hermes-telegram",
-            Platform.DISCORD: "hermes-discord",
-            Platform.WHATSAPP: "hermes-whatsapp",
-            Platform.SLACK: "hermes-slack",
-            Platform.SIGNAL: "hermes-signal",
-            Platform.HOMEASSISTANT: "hermes-homeassistant",
-            Platform.EMAIL: "hermes-email",
-            Platform.DINGTALK: "hermes-dingtalk",
-        }
+        user_config = _load_gateway_config()
+        platform_key = _platform_config_key(source.platform)
 
-        # Try to load platform_toolsets from config
-        platform_toolsets_config = {}
-        try:
-            config_path = _hermes_home / 'config.yaml'
-            if config_path.exists():
-                import yaml
-                with open(config_path, 'r', encoding="utf-8") as f:
-                    user_config = yaml.safe_load(f) or {}
-                platform_toolsets_config = user_config.get("platform_toolsets", {})
-        except Exception as e:
-            logger.debug("Could not load platform_toolsets config: %s", e)
+        from hermes_cli.tools_config import _get_platform_tools
+        enabled_toolsets = sorted(_get_platform_tools(user_config, platform_key))
 
-        # Map platform enum to config key
-        platform_config_key = {
-            Platform.LOCAL: "cli",
-            Platform.TELEGRAM: "telegram",
-            Platform.DISCORD: "discord",
-            Platform.WHATSAPP: "whatsapp",
-            Platform.SLACK: "slack",
-            Platform.SIGNAL: "signal",
-            Platform.HOMEASSISTANT: "homeassistant",
-            Platform.EMAIL: "email",
-            Platform.DINGTALK: "dingtalk",
-        }.get(source.platform, "telegram")
-        
-        # Use config override if present (list of toolsets), otherwise hardcoded default
-        config_toolsets = platform_toolsets_config.get(platform_config_key)
-        if config_toolsets and isinstance(config_toolsets, list):
-            enabled_toolsets = config_toolsets
-        else:
-            default_toolset = default_toolset_map.get(source.platform, "hermes-telegram")
-            enabled_toolsets = [default_toolset]
-        
         # Tool progress mode from config.yaml: "all", "new", "verbose", "off"
         # Falls back to env vars for backward compatibility
-        _progress_cfg = {}
-        try:
-            _tp_cfg_path = _hermes_home / "config.yaml"
-            if _tp_cfg_path.exists():
-                import yaml as _tp_yaml
-                with open(_tp_cfg_path, encoding="utf-8") as _tp_f:
-                    _tp_data = _tp_yaml.safe_load(_tp_f) or {}
-                _progress_cfg = _tp_data.get("display", {})
-        except Exception:
-            pass
         progress_mode = (
-            _progress_cfg.get("tool_progress")
+            user_config.get("display", {}).get("tool_progress")
             or os.getenv("HERMES_TOOL_PROGRESS_MODE")
             or "all"
         )
@@ -5025,7 +4945,7 @@ class GatewayRunner:
             except Exception:
                 pass
 
-            model = _resolve_gateway_model()
+            model = _resolve_gateway_model(user_config)
 
             try:
                 runtime_kwargs = _resolve_runtime_agent_kwargs()

hermes_cli/tools_config.py

@@ -131,6 +131,7 @@ PLATFORMS = {
     "slack":    {"label": "💼 Slack",      "default_toolset": "hermes-slack"},
     "whatsapp": {"label": "📱 WhatsApp",   "default_toolset": "hermes-whatsapp"},
     "signal":   {"label": "📡 Signal",     "default_toolset": "hermes-signal"},
+    "homeassistant": {"label": "🏠 Home Assistant", "default_toolset": "hermes-homeassistant"},
     "email":    {"label": "📧 Email",      "default_toolset": "hermes-email"},
     "dingtalk": {"label": "💬 DingTalk",   "default_toolset": "hermes-dingtalk"},
 }
@@ -378,7 +379,29 @@ def _platform_toolset_summary(config: dict, platforms: Optional[List[str]] = Non
     return summary
 
 
-def _get_platform_tools(config: dict, platform: str) -> Set[str]:
+def _parse_enabled_flag(value, default: bool = True) -> bool:
+    """Parse bool-like config values used by tool/platform settings."""
+    if value is None:
+        return default
+    if isinstance(value, bool):
+        return value
+    if isinstance(value, int):
+        return value != 0
+    if isinstance(value, str):
+        lowered = value.strip().lower()
+        if lowered in {"true", "1", "yes", "on"}:
+            return True
+        if lowered in {"false", "0", "no", "off"}:
+            return False
+    return default
+
+
+def _get_platform_tools(
+    config: dict,
+    platform: str,
+    *,
+    include_default_mcp_servers: bool = True,
+) -> Set[str]:
     """Resolve which individual toolset names are enabled for a platform."""
     from toolsets import resolve_toolset
 
@@ -430,6 +453,37 @@ def _get_platform_tools(config: dict, platform: str) -> Set[str]:
                 enabled_toolsets.add(pts)
             # else: known but not in config = user disabled it
 
+    # Preserve any explicit non-configurable toolset entries (for example,
+    # custom toolsets or MCP server names saved in platform_toolsets).
+    platform_default_keys = {p["default_toolset"] for p in PLATFORMS.values()}
+    explicit_passthrough = {
+        ts
+        for ts in toolset_names
+        if ts not in configurable_keys
+        and ts not in plugin_ts_keys
+        and ts not in platform_default_keys
+    }
+
+    # MCP servers are expected to be available on all platforms by default.
+    # If the platform explicitly lists one or more MCP server names, treat that
+    # as an allowlist. Otherwise include every globally enabled MCP server.
+    mcp_servers = config.get("mcp_servers", {})
+    enabled_mcp_servers = {
+        name
+        for name, server_cfg in mcp_servers.items()
+        if isinstance(server_cfg, dict)
+        and _parse_enabled_flag(server_cfg.get("enabled", True), default=True)
+    }
+    explicit_mcp_servers = explicit_passthrough & enabled_mcp_servers
+    enabled_toolsets.update(explicit_passthrough - enabled_mcp_servers)
+    if include_default_mcp_servers:
+        if explicit_mcp_servers:
+            enabled_toolsets.update(explicit_mcp_servers)
+        else:
+            enabled_toolsets.update(enabled_mcp_servers)
+    else:
+        enabled_toolsets.update(explicit_mcp_servers)
+
     return enabled_toolsets
 
 
@@ -1022,7 +1076,7 @@ def tools_command(args=None, first_install: bool = False, config: dict = None):
     if first_install:
         for pkey in enabled_platforms:
             pinfo = PLATFORMS[pkey]
-            current_enabled = _get_platform_tools(config, pkey)
+            current_enabled = _get_platform_tools(config, pkey, include_default_mcp_servers=False)
 
             # Uncheck toolsets that should be off by default
             checklist_preselected = current_enabled - _DEFAULT_OFF_TOOLSETS
@@ -1074,7 +1128,7 @@ def tools_command(args=None, first_install: bool = False, config: dict = None):
     platform_keys = []
     for pkey in enabled_platforms:
         pinfo = PLATFORMS[pkey]
-        current = _get_platform_tools(config, pkey)
+        current = _get_platform_tools(config, pkey, include_default_mcp_servers=False)
         count = len(current)
         total = len(_get_effective_configurable_toolsets())
         platform_choices.append(f"Configure {pinfo['label']}  ({count}/{total} enabled)")
@@ -1121,11 +1175,11 @@ def tools_command(args=None, first_install: bool = False, config: dict = None):
             # Use the union of all platforms' current tools as the starting state
             all_current = set()
             for pk in platform_keys:
-                all_current |= _get_platform_tools(config, pk)
+                all_current |= _get_platform_tools(config, pk, include_default_mcp_servers=False)
             new_enabled = _prompt_toolset_checklist("All platforms", all_current)
             if new_enabled != all_current:
                 for pk in platform_keys:
-                    prev = _get_platform_tools(config, pk)
+                    prev = _get_platform_tools(config, pk, include_default_mcp_servers=False)
                     added = new_enabled - prev
                     removed = prev - new_enabled
                     pinfo_inner = PLATFORMS[pk]
@@ -1147,7 +1201,7 @@ def tools_command(args=None, first_install: bool = False, config: dict = None):
                 print(color("  ✓ Saved configuration for all platforms", Colors.GREEN))
                 # Update choice labels
                 for ci, pk in enumerate(platform_keys):
-                    new_count = len(_get_platform_tools(config, pk))
+                    new_count = len(_get_platform_tools(config, pk, include_default_mcp_servers=False))
                     total = len(_get_effective_configurable_toolsets())
                     platform_choices[ci] = f"Configure {PLATFORMS[pk]['label']}  ({new_count}/{total} enabled)"
             else:
@@ -1159,7 +1213,7 @@ def tools_command(args=None, first_install: bool = False, config: dict = None):
         pinfo = PLATFORMS[pkey]
 
         # Get current enabled toolsets for this platform
-        current_enabled = _get_platform_tools(config, pkey)
+        current_enabled = _get_platform_tools(config, pkey, include_default_mcp_servers=False)
 
         # Show checklist
         new_enabled = _prompt_toolset_checklist(pinfo["label"], current_enabled)
@@ -1192,7 +1246,7 @@ def tools_command(args=None, first_install: bool = False, config: dict = None):
         print()
 
         # Update the choice label with new count
-        new_count = len(_get_platform_tools(config, pkey))
+        new_count = len(_get_platform_tools(config, pkey, include_default_mcp_servers=False))
         total = len(_get_effective_configurable_toolsets())
         platform_choices[idx] = f"Configure {pinfo['label']}  ({new_count}/{total} enabled)"
 
@@ -1338,7 +1392,7 @@ def _configure_mcp_tools_interactive(config: dict):
 
 def _apply_toolset_change(config: dict, platform: str, toolset_names: List[str], action: str):
     """Add or remove built-in toolsets for a platform."""
-    enabled = _get_platform_tools(config, platform)
+    enabled = _get_platform_tools(config, platform, include_default_mcp_servers=False)
     if action == "disable":
         updated = enabled - set(toolset_names)
     else:
@@ -1424,7 +1478,7 @@ def tools_disable_enable_command(args):
         return
 
     if action == "list":
-        _print_tools_list(_get_platform_tools(config, platform),
+        _print_tools_list(_get_platform_tools(config, platform, include_default_mcp_servers=False),
                           config.get("mcp_servers") or {}, platform)
         return
 

tests/gateway/test_reasoning_command.py

@@ -218,3 +218,112 @@ class TestReasoningCommand:
         assert result["final_response"] == "ok"
         assert _CapturingAgent.last_init is not None
         assert _CapturingAgent.last_init["reasoning_config"] == {"enabled": False}
+
+    def test_run_agent_includes_enabled_mcp_servers_in_gateway_toolsets(self, tmp_path, monkeypatch):
+        hermes_home = tmp_path / "hermes"
+        hermes_home.mkdir()
+        (hermes_home / "config.yaml").write_text(
+            "platform_toolsets:\n"
+            "  cli: [web, memory]\n"
+            "mcp_servers:\n"
+            "  exa:\n"
+            "    url: https://mcp.exa.ai/mcp\n"
+            "  web-search-prime:\n"
+            "    url: https://api.z.ai/api/mcp/web_search_prime/mcp\n",
+            encoding="utf-8",
+        )
+
+        monkeypatch.setattr(gateway_run, "_hermes_home", hermes_home)
+        monkeypatch.setattr(gateway_run, "_env_path", hermes_home / ".env")
+        monkeypatch.setattr(gateway_run, "load_dotenv", lambda *args, **kwargs: None)
+        monkeypatch.setattr(
+            gateway_run,
+            "_resolve_runtime_agent_kwargs",
+            lambda: {
+                "provider": "openrouter",
+                "api_mode": "chat_completions",
+                "base_url": "https://openrouter.ai/api/v1",
+                "api_key": "test-key",
+            },
+        )
+        fake_run_agent = types.ModuleType("run_agent")
+        fake_run_agent.AIAgent = _CapturingAgent
+        monkeypatch.setitem(sys.modules, "run_agent", fake_run_agent)
+
+        _CapturingAgent.last_init = None
+        runner = _make_runner()
+
+        source = SessionSource(
+            platform=Platform.LOCAL,
+            chat_id="cli",
+            chat_name="CLI",
+            chat_type="dm",
+            user_id="user-1",
+        )
+
+        result = asyncio.run(
+            runner._run_agent(
+                message="ping",
+                context_prompt="",
+                history=[],
+                source=source,
+                session_id="session-1",
+                session_key="agent:main:local:dm",
+            )
+        )
+
+        assert result["final_response"] == "ok"
+        assert _CapturingAgent.last_init is not None
+        enabled_toolsets = set(_CapturingAgent.last_init["enabled_toolsets"])
+        assert "web" in enabled_toolsets
+        assert "memory" in enabled_toolsets
+        assert "exa" in enabled_toolsets
+        assert "web-search-prime" in enabled_toolsets
+
+    def test_run_agent_homeassistant_uses_default_platform_toolset(self, tmp_path, monkeypatch):
+        hermes_home = tmp_path / "hermes"
+        hermes_home.mkdir()
+        (hermes_home / "config.yaml").write_text("", encoding="utf-8")
+
+        monkeypatch.setattr(gateway_run, "_hermes_home", hermes_home)
+        monkeypatch.setattr(gateway_run, "_env_path", hermes_home / ".env")
+        monkeypatch.setattr(gateway_run, "load_dotenv", lambda *args, **kwargs: None)
+        monkeypatch.setattr(
+            gateway_run,
+            "_resolve_runtime_agent_kwargs",
+            lambda: {
+                "provider": "openrouter",
+                "api_mode": "chat_completions",
+                "base_url": "https://openrouter.ai/api/v1",
+                "api_key": "test-key",
+            },
+        )
+        fake_run_agent = types.ModuleType("run_agent")
+        fake_run_agent.AIAgent = _CapturingAgent
+        monkeypatch.setitem(sys.modules, "run_agent", fake_run_agent)
+
+        _CapturingAgent.last_init = None
+        runner = _make_runner()
+
+        source = SessionSource(
+            platform=Platform.HOMEASSISTANT,
+            chat_id="ha",
+            chat_name="Home Assistant",
+            chat_type="dm",
+            user_id="user-1",
+        )
+
+        result = asyncio.run(
+            runner._run_agent(
+                message="ping",
+                context_prompt="",
+                history=[],
+                source=source,
+                session_id="session-1",
+                session_key="agent:main:homeassistant:dm",
+            )
+        )
+
+        assert result["final_response"] == "ok"
+        assert _CapturingAgent.last_init is not None
+        assert "homeassistant" in set(_CapturingAgent.last_init["enabled_toolsets"])

tests/hermes_cli/test_tools_config.py

@@ -35,6 +35,39 @@ def test_platform_toolset_summary_uses_explicit_platform_list():
     assert summary["cli"] == _get_platform_tools(config, "cli")
 
 
+def test_get_platform_tools_includes_enabled_mcp_servers_by_default():
+    config = {
+        "mcp_servers": {
+            "exa": {"url": "https://mcp.exa.ai/mcp"},
+            "web-search-prime": {"url": "https://api.z.ai/api/mcp/web_search_prime/mcp"},
+            "disabled-server": {"url": "https://example.com/mcp", "enabled": False},
+        }
+    }
+
+    enabled = _get_platform_tools(config, "cli")
+
+    assert "exa" in enabled
+    assert "web-search-prime" in enabled
+    assert "disabled-server" not in enabled
+
+
+def test_get_platform_tools_keeps_enabled_mcp_servers_with_explicit_builtin_selection():
+    config = {
+        "platform_toolsets": {"cli": ["web", "memory"]},
+        "mcp_servers": {
+            "exa": {"url": "https://mcp.exa.ai/mcp"},
+            "web-search-prime": {"url": "https://api.z.ai/api/mcp/web_search_prime/mcp"},
+        },
+    }
+
+    enabled = _get_platform_tools(config, "cli")
+
+    assert "web" in enabled
+    assert "memory" in enabled
+    assert "exa" in enabled
+    assert "web-search-prime" in enabled
+
+
 def test_toolset_has_keys_for_vision_accepts_codex_auth(tmp_path, monkeypatch):
     monkeypatch.setenv("HERMES_HOME", str(tmp_path))
     (tmp_path / "auth.json").write_text(

tests/hermes_cli/test_tools_disable_enable.py

@@ -134,6 +134,23 @@ class TestToolsMixedTargets:
         assert "web" not in saved["platform_toolsets"]["cli"]
         assert "create_issue" in saved["mcp_servers"]["github"]["tools"]["exclude"]
 
+    def test_builtin_toggle_does_not_persist_implicit_mcp_defaults(self):
+        config = {
+            "platform_toolsets": {"cli": ["web", "memory"]},
+            "mcp_servers": {"exa": {"url": "https://mcp.exa.ai/mcp"}},
+        }
+        with patch("hermes_cli.tools_config.load_config", return_value=config), \
+             patch("hermes_cli.tools_config.save_config") as mock_save:
+            tools_disable_enable_command(Namespace(
+                tools_action="disable",
+                names=["web"],
+                platform="cli",
+            ))
+        saved = mock_save.call_args[0][0]
+        assert "web" not in saved["platform_toolsets"]["cli"]
+        assert "memory" in saved["platform_toolsets"]["cli"]
+        assert "exa" not in saved["platform_toolsets"]["cli"]
+
 
 # ── List output ──────────────────────────────────────────────────────────────