diff --git a/navi/core/agent.py b/navi/core/agent.py
index 0c3b966..5b40dd0 100644
--- a/navi/core/agent.py
+++ b/navi/core/agent.py
@@ -182,7 +182,7 @@
             raise SessionNotFound(session_id)
 
         profile = self._profiles.get(session.profile_id)
-        tools = self._tool_list(profile.enabled_tools, profile.mcp_servers)
+        tools = self._tool_list(profile.get_agent_tools())
         tool_schemas = [t.schema() for t in tools]
         llm = self._get_backend(profile.llm_backend)
 
@@ -399,7 +399,7 @@
             if fresh and fresh.profile_id != session.profile_id:
                 session.profile_id = fresh.profile_id
                 profile = self._profiles.get(session.profile_id)
-                tools = self._tool_list(profile.enabled_tools, profile.mcp_servers)
+                tools = self._tool_list(profile.get_agent_tools())
                 tool_schemas = [t.schema() for t in tools]
                 llm = self._get_backend(profile.llm_backend)
                 log.info(
@@ -494,10 +494,9 @@
 
     def _tool_list(
         self,
-        enabled: list[str],
-        mcp_servers: dict[str, list[str]] | None = None,
+        scope: "ToolScopeConfig",
     ) -> list[Tool]:
-        return build_tool_list(enabled, mcp_servers, self._tools, self._mcp_manager)
+        return build_tool_list(scope.native, scope.mcp, self._tools, self._mcp_manager)
 
     def _get_backend(self, backend_key: str) -> LLMBackend:
         return self._backends.get(backend_key)
diff --git a/navi/core/context_builder.py b/navi/core/context_builder.py
index ca56719..2145d59 100644
--- a/navi/core/context_builder.py
+++ b/navi/core/context_builder.py
@@ -249,9 +249,9 @@
         """
         if not self._mcp_manager:
             return None
-        if profile is not None and not profile.mcp_servers:
+        if profile is not None and not profile.get_agent_tools().mcp:
             return None
-        server_names = set(profile.mcp_servers.keys()) if profile is not None else None
+        server_names = set(profile.get_agent_tools().mcp.keys()) if profile is not None else None
         instructions = self._mcp_manager.get_instructions(server_names)
         if not instructions:
             return None
diff --git a/navi/core/subagent_runner.py b/navi/core/subagent_runner.py
index f269bea..2cfc397 100644
--- a/navi/core/subagent_runner.py
+++ b/navi/core/subagent_runner.py
@@ -100,32 +100,10 @@
         _model_var.set(profile.model)
         exclude = set(exclude_tools or [])
 
-        from navi.mcp.tools import build_mcp_name, is_mcp_tool
-
-        tool_source = profile.subagent_tools if profile.subagent_tools else profile.enabled_tools
-
-        # If subagent_tools is a strict whitelist, filter mcp_servers to only
-        # include MCP tools explicitly listed in the whitelist.  This prevents
-        # a profile from accidentally granting sub-agents access to MCP servers
-        # that are meant for the main agent only.
-        mcp_servers = profile.mcp_servers
-        if profile.subagent_tools:
-            mcp_tool_names = {n for n in profile.subagent_tools if is_mcp_tool(n)}
-            if mcp_tool_names:
-                filtered_mcp_servers: dict[str, list[str]] = {}
-                for server_name, groups in (profile.mcp_servers or {}).items():
-                    for group_name in groups:
-                        for tool_name in self._mcp_manager.resolve_group(server_name, group_name):
-                            full_name = build_mcp_name(server_name, tool_name)
-                            if full_name in mcp_tool_names:
-                                filtered_mcp_servers.setdefault(server_name, []).append(group_name)
-                mcp_servers = filtered_mcp_servers or None
-            else:
-                mcp_servers = None
-
+        scope = profile.get_subagent_tools()
         tools = [
             t
-            for t in build_tool_list(tool_source, mcp_servers, self._tools, self._mcp_manager)
+            for t in build_tool_list(scope.native, scope.mcp, self._tools, self._mcp_manager)
             if t.name not in exclude
         ]
         tool_schemas = [t.schema() for t in tools]
diff --git a/navi/profiles/base.py b/navi/profiles/base.py
index fabbbc2..d030d75 100644
--- a/navi/profiles/base.py
+++ b/navi/profiles/base.py
@@ -1,4 +1,18 @@
-from pydantic import BaseModel, Field, field_validator
+from pydantic import BaseModel, Field, field_validator, model_validator
+
+
+class ToolScopeConfig(BaseModel):
+    """Tool set for a single scope (agent or subagent)."""
+
+    native: list[str] = Field(default_factory=list)
+    mcp: dict[str, list[str]] = Field(default_factory=dict)
+
+
+class ToolConfig(BaseModel):
+    """Explicit per-profile tool configuration."""
+
+    agent: ToolScopeConfig = Field(default_factory=ToolScopeConfig)
+    subagent: ToolScopeConfig = Field(default_factory=ToolScopeConfig)
 
 
 class AgentProfile(BaseModel):
@@ -14,7 +28,15 @@
     name: str
     description: str
     system_prompt: str
-    enabled_tools: list[str]  # tool names; resolved by ToolRegistry at runtime
+    tools: ToolConfig = Field(default_factory=ToolConfig)
+
+    # --- Deprecated: kept for auto-migration from old configs ------------------
+    # These fields are automatically migrated into ``tools`` by the loader.
+    # Do not set them in new configs; use ``tools.agent`` / ``tools.subagent``.
+    enabled_tools: list[str] = Field(default_factory=list)
+    mcp_servers: dict[str, list[str]] = Field(default_factory=dict)
+    subagent_tools: list[str] = Field(default_factory=list)
+
     llm_backend: str = "ollama"  # backend key, e.g. "ollama", "openai"
     # Ordered list of preferred models; first available wins at runtime.
     # Accepts a plain string for backward compatibility (auto-wrapped in a list).
@@ -91,14 +113,8 @@
     adaptive_replan_enabled: bool = False
 
     # Sub-agent configuration
-    # subagent_tools: tool names available to sub-agents spawned from this profile.
-    #   If empty, falls back to enabled_tools minus dangerous/irrelevant ones.
-    # subagent_planning_enabled: if True, sub-agents run the planning phase before their tool loop.
-    # subagent_think_enabled: controls extended reasoning for sub-agents. If None,
-    #   sub-agents inherit think_enabled from the parent profile.
     # subagent_system_prompt: injected as an additional system message for sub-agents,
     #   after the profile's main system_prompt. Loaded from subagent_system_prompt.txt if present.
-    subagent_tools: list[str] = Field(default_factory=list)
     subagent_planning_enabled: bool = False
     subagent_think_enabled: bool | None = None
     subagent_system_prompt: str = ""
@@ -107,13 +123,45 @@
     # Global providers (global_provider=True) are always injected regardless of this list.
     context_providers: list[str] = Field(default_factory=list)
 
-    # MCP servers referenced by this profile.
-    # Format: {"server_name": ["group1", "group2"]} or {"server_name": ["*"]} for all tools.
-    mcp_servers: dict[str, list[str]] = Field(default_factory=dict)
-
     @field_validator("model", mode="before")
     @classmethod
     def _coerce_model(cls, v):
         if isinstance(v, str):
             return [v] if v else ["gemma4:31b-cloud"]
         return v
+
+    @model_validator(mode="after")
+    def _migrate_tools(self):
+        """Auto-migrate legacy fields into the explicit ``tools`` structure."""
+        if self.enabled_tools or self.mcp_servers or self.subagent_tools:
+            if not self.tools.agent.native:
+                self.tools.agent.native = list(self.enabled_tools)
+            if not self.tools.agent.mcp:
+                self.tools.agent.mcp = dict(self.mcp_servers)
+            if self.subagent_tools:
+                if not self.tools.subagent.native:
+                    self.tools.subagent.native = list(self.subagent_tools)
+                if not self.tools.subagent.mcp:
+                    # Infer MCP servers from subagent_tools if they contain mcp__ names
+                    from navi.mcp.tools import is_mcp_tool
+                    inferred: dict[str, list[str]] = {}
+                    for name in self.subagent_tools:
+                        if is_mcp_tool(name):
+                            # e.g. mcp__navi_3d__compile_scad -> server navi_3d
+                            parts = name.split("__", 2)
+                            if len(parts) >= 2:
+                                srv = parts[1]
+                                inferred.setdefault(srv, []).append("*")
+                    self.tools.subagent.mcp = inferred
+        return self
+
+    def get_agent_tools(self) -> ToolScopeConfig:
+        """Return the resolved agent tool set."""
+        return self.tools.agent
+
+    def get_subagent_tools(self) -> ToolScopeConfig:
+        """Return the resolved subagent tool set."""
+        if self.tools.subagent.native or self.tools.subagent.mcp:
+            return self.tools.subagent
+        # Fallback: if subagent is empty but agent is not, use agent
+        return self.tools.agent
diff --git a/navi/profiles/developer/config.json b/navi/profiles/developer/config.json
index 495b66f..4456d1d 100644
--- a/navi/profiles/developer/config.json
+++ b/navi/profiles/developer/config.json
@@ -10,6 +10,7 @@
   },
   "llm_backend": "ollama",
   "model": [
+    "qwen3.5:397b-cloud",
     "gemma4:26b-a4b-it-q4_K_M",
     "gemma4:31b-cloud",
     "kimi-k2.6:cloud",
@@ -27,39 +28,6 @@
   "anti_stall_threshold": 8,
   "step_validation_enabled": false,
   "adaptive_replan_enabled": true,
-  "subagent_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "image_view",
-    "list_tools",
-    "share_file",
-    "content_publish"
-  ],
-  "enabled_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "switch_profile",
-    "list_profiles",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "image_view",
-    "memory",
-    "list_tools",
-    "tool_manual",
-    "ssh_exec",
-    "spawn_agent",
-    "share_file",
-    "content_publish",
-    "gmail",
-    "schedule_recall",
-    "manage_recall"
-  ],
   "planning_mandatory": false,
   "planning_phase1_enabled": true,
   "planning_phase2_enabled": true,
@@ -67,11 +35,51 @@
   "top_k": 40,
   "top_p": 0.88,
   "num_thread": 11,
-  "mcp_servers": {
-    "navi-web": [
-      "search",
-      "browse",
-      "request"
-    ]
+  "tools": {
+    "agent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "switch_profile",
+        "list_profiles",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "image_view",
+        "memory",
+        "list_tools",
+        "tool_manual",
+        "ssh_exec",
+        "spawn_agent",
+        "share_file",
+        "content_publish",
+        "gmail",
+        "schedule_recall",
+        "manage_recall"
+      ],
+      "mcp": {
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    },
+    "subagent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "image_view",
+        "list_tools",
+        "share_file",
+        "content_publish"
+      ],
+      "mcp": {}
+    }
   }
 }
diff --git a/navi/profiles/discuss/config.json b/navi/profiles/discuss/config.json
index 3d41119..d7595b3 100644
--- a/navi/profiles/discuss/config.json
+++ b/navi/profiles/discuss/config.json
@@ -4,6 +4,7 @@
   "description": "Creative partner for Q&A, brainstorming, and idea exploration. High creativity, free-form thinking.",
   "short_description": "Creative Q&A and idea discussion — best for open questions, brainstorming, and exploring concepts.",
   "model": [
+    "qwen3.5:397b-cloud",
     "gemma4:26b-a4b-it-q4_K_M",
     "gemma4:31b-cloud",
     "kimi-k2.6:cloud",
@@ -11,33 +12,6 @@
   ],
   "temperature": 0.65,
   "max_iterations": 30,
-  "enabled_tools": [
-    "scratchpad",
-    "reflect",
-    "memory",
-    "image_view",
-    "todo",
-    "get_current_datetime",
-    "list_tools",
-    "tool_manual",
-    "switch_profile",
-    "list_profiles",
-    "share_file",
-    "filesystem",
-    "schedule_recall",
-    "manage_recall"
-  ],
-  "mcp_servers": {
-    "gnexus-book": [
-      "read"
-    ],
-    "navi-web": [
-      "search",
-      "browse",
-      "request"
-    ]
-  },
-  "subagent_tools": [],
   "planning_enabled": false,
   "planning_mandatory": false,
   "planning_phase1_enabled": true,
@@ -54,5 +28,39 @@
   "subagent_planning_enabled": false,
   "top_k": 80,
   "top_p": 0.95,
-  "num_thread": 11
+  "num_thread": 11,
+  "tools": {
+    "agent": {
+      "native": [
+        "scratchpad",
+        "reflect",
+        "memory",
+        "image_view",
+        "todo",
+        "get_current_datetime",
+        "list_tools",
+        "tool_manual",
+        "switch_profile",
+        "list_profiles",
+        "share_file",
+        "filesystem",
+        "schedule_recall",
+        "manage_recall"
+      ],
+      "mcp": {
+        "gnexus-book": [
+          "read"
+        ],
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    },
+    "subagent": {
+      "native": [],
+      "mcp": {}
+    }
+  }
 }
diff --git a/navi/profiles/loader.py b/navi/profiles/loader.py
index a4b5c34..b988918 100644
--- a/navi/profiles/loader.py
+++ b/navi/profiles/loader.py
@@ -12,11 +12,11 @@
 import structlog
 from pathlib import Path
 
-from .base import AgentProfile
+from .base import AgentProfile, ToolConfig
 
 log = structlog.get_logger()
 
-_REQUIRED_CONFIG_KEYS = {"id", "name", "description", "enabled_tools"}
+_REQUIRED_CONFIG_KEYS = {"id", "name", "description"}
 
 
 def _normalize_model(value: object) -> list[str]:
@@ -63,12 +63,24 @@
             # If only the old key is present, migrate its value transparently.
             phase2_default = config.get("planning_reflect_enabled", False)
 
+            # New explicit tool config or legacy migration
+            _tools_raw = config.get("tools")
+            _tools = ToolConfig.model_validate(_tools_raw) if _tools_raw else ToolConfig()
+
+            # Legacy fields still accepted for auto-migration
+            _enabled_tools = config.get("enabled_tools", [])
+            _mcp_servers = config.get("mcp_servers", {})
+            _subagent_tools = config.get("subagent_tools", [])
+
             profiles.append(AgentProfile(
                 id=config["id"],
                 name=config["name"],
                 description=config["description"],
                 system_prompt=system_prompt,
-                enabled_tools=config["enabled_tools"],
+                tools=_tools,
+                enabled_tools=_enabled_tools,
+                mcp_servers=_mcp_servers,
+                subagent_tools=_subagent_tools,
                 llm_backend=config.get("llm_backend", "ollama"),
                 model=_normalize_model(config.get("model", ["gemma4:31b-cloud"])),
                 temperature=config.get("temperature", 0.7),
@@ -92,12 +104,10 @@
                 anti_stall_threshold=config.get("anti_stall_threshold", 8),
                 step_validation_enabled=config.get("step_validation_enabled", False),
                 adaptive_replan_enabled=config.get("adaptive_replan_enabled", False),
-                subagent_tools=config.get("subagent_tools", []),
                 subagent_planning_enabled=config.get("subagent_planning_enabled", False),
                 subagent_think_enabled=config.get("subagent_think_enabled", None),
                 subagent_system_prompt=subagent_system_prompt,
                 context_providers=config.get("context_providers", []),
-                mcp_servers=config.get("mcp_servers", {}),
             ))
             log.debug("profile.loader.loaded", profile_id=config["id"])
 
@@ -143,13 +153,11 @@
         "anti_stall_threshold": profile.anti_stall_threshold,
         "step_validation_enabled": profile.step_validation_enabled,
         "adaptive_replan_enabled": profile.adaptive_replan_enabled,
-        "subagent_tools": profile.subagent_tools,
         "subagent_planning_enabled": profile.subagent_planning_enabled,
         "subagent_think_enabled": profile.subagent_think_enabled,
         "is_subagent_only": profile.is_subagent_only,
-        "enabled_tools": profile.enabled_tools,
+        "tools": profile.tools.model_dump(mode="json"),
         "context_providers": profile.context_providers,
-        "mcp_servers": profile.mcp_servers,
     }
 
     config_file = profile_dir / "config.json"
diff --git a/navi/profiles/modeler_3d/config.json b/navi/profiles/modeler_3d/config.json
index 94e1d6d..2c3a9f9 100644
--- a/navi/profiles/modeler_3d/config.json
+++ b/navi/profiles/modeler_3d/config.json
@@ -10,9 +10,12 @@
   },
   "llm_backend": "ollama",
   "model": [
+    "glm-5.1:cloud",
+    "qwen3.5:397b-cloud",
+    "kimi-k2.6:cloud",
     "gemma4:26b-a4b-it-q4_K_M",
     "gemma4:31b-cloud",
-    "qwen3.6:27b"
+    "qwen3.6:35b"
   ],
   "temperature": 0.35,
   "max_iterations": 70,
@@ -31,41 +34,48 @@
   "adaptive_replan_enabled": true,
   "subagent_planning_enabled": false,
   "subagent_think_enabled": false,
-  "subagent_tools": [
-    "filesystem",
-    "image_view"
-  ],
-  "enabled_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "switch_profile",
-    "list_profiles",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "image_view",
-    "memory",
-    "list_tools",
-    "tool_manual",
-    "spawn_agent",
-    "share_file",
-    "content_publish",
-    "schedule_recall",
-    "manage_recall"
-  ],
-  "mcp_servers": {
-    "navi-3d": [
-      "modeling",
-      "analysis"
-    ],
-    "navi-web": [
-      "search",
-      "browse",
-      "request"
-    ]
-  },
   "top_k": 30,
   "top_p": 0.85,
-  "num_thread": 11
+  "num_thread": 11,
+  "tools": {
+    "agent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "switch_profile",
+        "list_profiles",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "image_view",
+        "memory",
+        "list_tools",
+        "tool_manual",
+        "spawn_agent",
+        "share_file",
+        "content_publish",
+        "schedule_recall",
+        "manage_recall"
+      ],
+      "mcp": {
+        "navi-3d": [
+          "modeling",
+          "analysis"
+        ],
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    },
+    "subagent": {
+      "native": [
+        "filesystem",
+        "image_view"
+      ],
+      "mcp": {}
+    }
+  }
 }
diff --git a/navi/profiles/secretary/config.json b/navi/profiles/secretary/config.json
index 65316d2..4da42e2 100644
--- a/navi/profiles/secretary/config.json
+++ b/navi/profiles/secretary/config.json
@@ -10,6 +10,7 @@
   },
   "llm_backend": "ollama",
   "model": [
+    "qwen3.5:397b-cloud",
     "kimi-k2.6:cloud",
     "gemma4:26b-a4b-it-q4_K_M",
     "gemma4:31b-cloud",
@@ -27,36 +28,6 @@
   "anti_stall_threshold": 8,
   "step_validation_enabled": false,
   "adaptive_replan_enabled": false,
-  "subagent_tools": [
-    "scratchpad",
-    "reflect",
-    "filesystem",
-    "code_exec",
-    "image_view",
-    "memory",
-    "share_file",
-    "content_publish"
-  ],
-  "enabled_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "switch_profile",
-    "list_profiles",
-    "filesystem",
-    "code_exec",
-    "image_view",
-    "memory",
-    "list_tools",
-    "tool_manual",
-    "spawn_agent",
-    "share_file",
-    "content_publish",
-    "weather",
-    "gmail",
-    "schedule_recall",
-    "manage_recall"
-  ],
   "planning_mandatory": false,
   "planning_phase1_enabled": true,
   "planning_phase2_enabled": true,
@@ -64,11 +35,54 @@
   "top_k": 50,
   "top_p": 0.9,
   "num_thread": 11,
-  "mcp_servers": {
-    "navi-web": [
-      "search",
-      "browse",
-      "request"
-    ]
+  "tools": {
+    "agent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "switch_profile",
+        "list_profiles",
+        "filesystem",
+        "code_exec",
+        "image_view",
+        "memory",
+        "list_tools",
+        "tool_manual",
+        "spawn_agent",
+        "share_file",
+        "content_publish",
+        "weather",
+        "gmail",
+        "schedule_recall",
+        "manage_recall"
+      ],
+      "mcp": {
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    },
+    "subagent": {
+      "native": [
+        "scratchpad",
+        "reflect",
+        "filesystem",
+        "code_exec",
+        "image_view",
+        "memory",
+        "share_file",
+        "content_publish"
+      ],
+      "mcp": {
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    }
   }
 }
diff --git a/navi/profiles/server_admin/config.json b/navi/profiles/server_admin/config.json
index 8087220..dd9c1ee 100644
--- a/navi/profiles/server_admin/config.json
+++ b/navi/profiles/server_admin/config.json
@@ -10,6 +10,7 @@
   },
   "llm_backend": "ollama",
   "model": [
+    "qwen3.5:397b-cloud",
     "gemma4:26b-a4b-it-q4_K_M",
     "gemma4:31b-cloud",
     "kimi-k2.6:cloud",
@@ -27,54 +28,61 @@
   "anti_stall_threshold": 8,
   "step_validation_enabled": false,
   "adaptive_replan_enabled": false,
-  "subagent_tools": [
-    "scratchpad",
-    "reflect",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "ssh_exec",
-    "image_view",
-    "share_file",
-    "content_publish"
-  ],
-  "enabled_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "switch_profile",
-    "list_profiles",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "ssh_exec",
-    "image_view",
-    "memory",
-    "list_tools",
-    "tool_manual",
-    "spawn_agent",
-    "share_file",
-    "content_publish",
-    "gmail",
-    "schedule_recall",
-    "manage_recall"
-  ],
-  "mcp_servers": {
-    "gnexus-book": [
-      "read",
-      "write"
-    ],
-    "navi-web": [
-      "search",
-      "browse",
-      "request"
-    ]
-  },
   "planning_mandatory": false,
   "planning_phase1_enabled": true,
   "planning_phase2_enabled": true,
   "planning_phase3_enabled": true,
   "top_k": 30,
   "top_p": 0.8,
-  "num_thread": 11
+  "num_thread": 11,
+  "tools": {
+    "agent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "switch_profile",
+        "list_profiles",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "ssh_exec",
+        "image_view",
+        "memory",
+        "list_tools",
+        "tool_manual",
+        "spawn_agent",
+        "share_file",
+        "content_publish",
+        "gmail",
+        "schedule_recall",
+        "manage_recall"
+      ],
+      "mcp": {
+        "gnexus-book": [
+          "read",
+          "write"
+        ],
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    },
+    "subagent": {
+      "native": [
+        "scratchpad",
+        "reflect",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "ssh_exec",
+        "image_view",
+        "share_file",
+        "content_publish"
+      ],
+      "mcp": {}
+    }
+  }
 }
diff --git a/navi/profiles/tool_developer/config.json b/navi/profiles/tool_developer/config.json
index 7371fcd..5c03668 100644
--- a/navi/profiles/tool_developer/config.json
+++ b/navi/profiles/tool_developer/config.json
@@ -10,6 +10,7 @@
   },
   "llm_backend": "ollama",
   "model": [
+    "qwen3.5:397b-cloud",
     "gemma4:26b-a4b-it-q4_K_M",
     "gemma4:31b-cloud",
     "kimi-k2.6:cloud",
@@ -27,55 +28,62 @@
   "anti_stall_threshold": 8,
   "step_validation_enabled": false,
   "adaptive_replan_enabled": true,
-  "subagent_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "image_view",
-    "list_tools",
-    "tool_manual",
-    "share_file",
-    "content_publish"
-  ],
-  "enabled_tools": [
-    "todo",
-    "scratchpad",
-    "reflect",
-    "switch_profile",
-    "list_profiles",
-    "filesystem",
-    "code_exec",
-    "terminal",
-    "image_view",
-    "memory",
-    "reload_tools",
-    "list_tools",
-    "tool_manual",
-    "spawn_agent",
-    "share_file",
-    "content_publish",
-    "gmail",
-    "create_mcp_server",
-    "test_mcp_tool",
-    "mcp_status",
-    "schedule_recall",
-    "manage_recall"
-  ],
   "planning_mandatory": false,
   "planning_phase1_enabled": true,
   "planning_phase2_enabled": true,
   "planning_phase3_enabled": true,
   "top_k": 40,
   "top_p": 0.85,
-  "mcp_servers": {
-    "navi-web": [
-      "search",
-      "browse",
-      "request"
-    ]
-  },
-  "num_thread": 11
+  "num_thread": 11,
+  "tools": {
+    "agent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "switch_profile",
+        "list_profiles",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "image_view",
+        "memory",
+        "reload_tools",
+        "list_tools",
+        "tool_manual",
+        "spawn_agent",
+        "share_file",
+        "content_publish",
+        "gmail",
+        "create_mcp_server",
+        "test_mcp_tool",
+        "mcp_status",
+        "schedule_recall",
+        "manage_recall"
+      ],
+      "mcp": {
+        "navi-web": [
+          "search",
+          "browse",
+          "request"
+        ]
+      }
+    },
+    "subagent": {
+      "native": [
+        "todo",
+        "scratchpad",
+        "reflect",
+        "filesystem",
+        "code_exec",
+        "terminal",
+        "image_view",
+        "list_tools",
+        "tool_manual",
+        "share_file",
+        "content_publish"
+      ],
+      "mcp": {}
+    }
+  }
 }
diff --git a/navi/tools/list_tools.py b/navi/tools/list_tools.py
index e2708e6..cc47f0f 100644
--- a/navi/tools/list_tools.py
+++ b/navi/tools/list_tools.py
@@ -57,15 +57,16 @@
             except Exception:
                 return ToolResult(success=False, output=f"Profile '{profile_id}' not found.", error="profile_not_found")
 
-            names = list(profile.enabled_tools)
+            scope = profile.get_agent_tools()
+            names = list(scope.native)
             extra = _load_user_enabled_tools()
             for name in extra:
                 if name not in names:
                     names.append(name)
 
             # Expand MCP server groups into concrete tool names
-            if profile.mcp_servers and self._mcp_manager:
-                for server_name, groups in profile.mcp_servers.items():
+            if scope.mcp and self._mcp_manager:
+                for server_name, groups in scope.mcp.items():
                     if "*" in groups:
                         prefix = build_mcp_name(server_name, "")
                         for tool in self._registry.all():
diff --git a/navi/tools/spawn_agent.py b/navi/tools/spawn_agent.py
index 04d7c8c..285449e 100644
--- a/navi/tools/spawn_agent.py
+++ b/navi/tools/spawn_agent.py
@@ -140,17 +140,13 @@
         parent_sid = current_session_id.get()
         context_transfer = (await get_section(parent_sid, "context_transfer")) if parent_sid else ""
 
-        tool_source = (
-            selected_profile.subagent_tools
-            if selected_profile.subagent_tools
-            else selected_profile.enabled_tools
-        )
+        scope = selected_profile.get_subagent_tools()
 
         log.info("spawn_agent.start", profile_id=profile_id, max_iterations=max_iterations,
                  task_preview=task[:80], has_briefing=bool(briefing),
                  has_context_transfer=bool(context_transfer),
                  has_system_prompt=bool(custom_system_prompt),
-                 subagent_tools=len(tool_source))
+                 subagent_tools=len(scope.native) + sum(len(v) for v in scope.mcp.values()))
 
         agent = Agent(
             session_store=None,          # ephemeral — no DB access