fix(mcp): treat tools.include: [] as an explicit empty whitelist

_normalize_name_filter([]) returns an empty set, which is falsy, so
_should_register fell through to "no filter" and registered every tool
— the exact opposite of what _apply_tool_selection wrote when the user
unchecked everything in the install checklist ("contributes nothing
until reconfigured"). Whitelist mode is now keyed on the include key
holding a valid filter shape (str/list/tuple/set) rather than on set
truthiness, at both the live-discovery and cached-manifest sites.
Invalid include values keep the old warn-and-ignore behaviour.

tests/tools/test_mcp_tool.py

@@ -2394,6 +2394,24 @@ class TestMCPSelectiveToolLoading:
         )
         assert registered == ["mcp__ink__create_service"]
 
+    def test_empty_include_registers_nothing(self):
+        """include: [] is an explicit empty whitelist, not "no filter".
+
+        The install checklist writes include: [] when the user unchecks
+        every tool ("contributes nothing until reconfigured") — the next
+        session must not register the full tool surface.
+        """
+        config = {
+            "url": "https://mcp.example.com",
+            "tools": {"include": []},
+        }
+        registered, _ = self._run_discover(
+            "ink",
+            ["create_service", "delete_service", "list_services"],
+            config,
+            session=SimpleNamespace(),
+        )
+        assert registered == []
 
     def test_enabled_false_skips_connection_attempt(self):
         from tools.mcp_tool import discover_mcp_tools

tools/mcp_tool.py

@@ -7125,17 +7125,21 @@ def _register_server_tools(name: str, server: MCPServerTask, config: dict) -> Li
     #   tools.exclude — blacklist: all tools EXCEPT matching ones are registered
     #   entries may be exact names or fnmatch globs (e.g. "*_radar_*")
     #   include takes precedence over exclude
+    #   include: [] → register nothing (an explicit empty whitelist, as
+    #   written by the install checklist's "uncheck everything" path)
     #   Neither set → register all tools (backward-compatible default)
     tools_filter = config.get("tools") or {}
+    include_raw = tools_filter.get("include")
     include_set = _normalize_name_filter(
-        tools_filter.get("include"), f"mcp_servers.{name}.tools.include"
+        include_raw, f"mcp_servers.{name}.tools.include"
     )
+    include_active = isinstance(include_raw, (str, list, tuple, set))
     exclude_set = _normalize_name_filter(
         tools_filter.get("exclude"), f"mcp_servers.{name}.tools.exclude"
     )
 
     def _should_register(tool_name: str) -> bool:
-        if include_set:
+        if include_active:
             return matches_name_filter(tool_name, include_set)
         if exclude_set:
             return not matches_name_filter(tool_name, exclude_set)
@@ -7389,15 +7393,19 @@ def _register_from_cache_sync(name: str, config: dict, entry: dict) -> List[str]
     fingerprint = config_fingerprint(config)
     tool_timeout = _resolve_tool_timeout(config)
     tools_filter = config.get("tools") or {}
+    include_raw = tools_filter.get("include")
     include_set = _normalize_name_filter(
-        tools_filter.get("include"), f"mcp_servers.{name}.tools.include"
+        include_raw, f"mcp_servers.{name}.tools.include"
     )
+    # include: [] is an explicit empty whitelist (register nothing) — see the
+    # live discovery path above for the full filter rules.
+    include_active = isinstance(include_raw, (str, list, tuple, set))
     exclude_set = _normalize_name_filter(
         tools_filter.get("exclude"), f"mcp_servers.{name}.tools.exclude"
     )
 
     def _should_register(tool_name: str) -> bool:
-        if include_set:
+        if include_active:
             return matches_name_filter(tool_name, include_set)
         if exclude_set:
             return not matches_name_filter(tool_name, exclude_set)