fix(core): ensure subagents use qualified MCP tool names (#20801)

packages/core/src/tools/tool-registry.test.ts

@@ -380,20 +380,36 @@ describe('ToolRegistry', () => {
   });
 
   describe('getAllToolNames', () => {
-    it('should return all registered tool names', () => {
+    it('should return all registered tool names with qualified names for MCP tools', () => {
       // Register tools with displayNames in non-alphabetical order
       const toolC = new MockTool({ name: 'c-tool', displayName: 'Tool C' });
       const toolA = new MockTool({ name: 'a-tool', displayName: 'Tool A' });
-      const toolB = new MockTool({ name: 'b-tool', displayName: 'Tool B' });
+      const mcpTool = createMCPTool('my-server', 'my-tool', 'desc');
 
       toolRegistry.registerTool(toolC);
       toolRegistry.registerTool(toolA);
-      toolRegistry.registerTool(toolB);
+      toolRegistry.registerTool(mcpTool);
 
       const toolNames = toolRegistry.getAllToolNames();
 
-      // Assert that the returned array contains all tool names
-      expect(toolNames).toEqual(['c-tool', 'a-tool', 'b-tool']);
+      // Assert that the returned array contains all tool names, with MCP qualified
+      expect(toolNames).toContain('c-tool');
+      expect(toolNames).toContain('a-tool');
+      expect(toolNames).toContain('my-server__my-tool');
+      expect(toolNames).toHaveLength(3);
+    });
+
+    it('should deduplicate tool names', () => {
+      const serverName = 'my-server';
+      const toolName = 'my-tool';
+      const mcpTool = createMCPTool(serverName, toolName, 'desc');
+
+      // Register same MCP tool twice (one as alias, one as qualified)
+      toolRegistry.registerTool(mcpTool);
+      toolRegistry.registerTool(mcpTool.asFullyQualifiedTool());
+
+      const toolNames = toolRegistry.getAllToolNames();
+      expect(toolNames).toEqual([`${serverName}__${toolName}`]);
     });
   });
 
@@ -465,8 +481,8 @@ describe('ToolRegistry', () => {
         'builtin-1',
         'builtin-2',
         DISCOVERED_TOOL_PREFIX + 'discovered-1',
-        'mcp-apple',
-        'mcp-zebra',
+        'apple-server__mcp-apple',
+        'zebra-server__mcp-zebra',
       ]);
     });
   });
@@ -659,6 +675,34 @@ describe('ToolRegistry', () => {
     });
   });
 
+  describe('getFunctionDeclarations', () => {
+    it('should use fully qualified names for MCP tools in declarations', () => {
+      const serverName = 'my-server';
+      const toolName = 'my-tool';
+      const mcpTool = createMCPTool(serverName, toolName, 'description');
+
+      toolRegistry.registerTool(mcpTool);
+
+      const declarations = toolRegistry.getFunctionDeclarations();
+      expect(declarations).toHaveLength(1);
+      expect(declarations[0].name).toBe(`${serverName}__${toolName}`);
+    });
+
+    it('should deduplicate MCP tools in declarations', () => {
+      const serverName = 'my-server';
+      const toolName = 'my-tool';
+      const mcpTool = createMCPTool(serverName, toolName, 'description');
+
+      // Register both alias and qualified
+      toolRegistry.registerTool(mcpTool);
+      toolRegistry.registerTool(mcpTool.asFullyQualifiedTool());
+
+      const declarations = toolRegistry.getFunctionDeclarations();
+      expect(declarations).toHaveLength(1);
+      expect(declarations[0].name).toBe(`${serverName}__${toolName}`);
+    });
+  });
+
   describe('plan mode', () => {
     it('should only return policy-allowed tools in plan mode', () => {
       // Register several tools

packages/core/src/tools/tool-registry.ts

@@ -539,11 +539,32 @@ export class ToolRegistry {
     const plansDir = this.config.storage.getPlansDir();
 
     const declarations: FunctionDeclaration[] = [];
+    const seenNames = new Set<string>();
+
     this.getActiveTools().forEach((tool) => {
+      const toolName =
+        tool instanceof DiscoveredMCPTool
+          ? tool.getFullyQualifiedName()
+          : tool.name;
+
+      if (seenNames.has(toolName)) {
+        return;
+      }
+      seenNames.add(toolName);
+
       let schema = tool.getSchema(modelId);
+
+      // Ensure the schema name matches the qualified name for MCP tools
+      if (tool instanceof DiscoveredMCPTool) {
+        schema = {
+          ...schema,
+          name: toolName,
+        };
+      }
+
       if (
         isPlanMode &&
-        (tool.name === WRITE_FILE_TOOL_NAME || tool.name === EDIT_TOOL_NAME)
+        (toolName === WRITE_FILE_TOOL_NAME || toolName === EDIT_TOOL_NAME)
       ) {
         schema = {
           ...schema,
@@ -576,20 +597,42 @@ export class ToolRegistry {
   }
 
   /**
-   * Returns an array of all registered and discovered tool names which are not
-   * excluded via configuration.
+   * Returns an array of names for all active tools.
+   * For MCP tools, this returns their fully qualified names.
+   * The list is deduplicated.
    */
   getAllToolNames(): string[] {
-    return this.getActiveTools().map((tool) => tool.name);
+    const names = new Set<string>();
+    for (const tool of this.getActiveTools()) {
+      if (tool instanceof DiscoveredMCPTool) {
+        names.add(tool.getFullyQualifiedName());
+      } else {
+        names.add(tool.name);
+      }
+    }
+    return Array.from(names);
   }
 
   /**
    * Returns an array of all registered and discovered tool instances.
    */
   getAllTools(): AnyDeclarativeTool[] {
-    return this.getActiveTools().sort((a, b) =>
+    const seen = new Set<string>();
+    const tools: AnyDeclarativeTool[] = [];
+
+    for (const tool of this.getActiveTools().sort((a, b) =>
       a.displayName.localeCompare(b.displayName),
-    );
+    )) {
+      const name =
+        tool instanceof DiscoveredMCPTool
+          ? tool.getFullyQualifiedName()
+          : tool.name;
+      if (!seen.has(name)) {
+        seen.add(name);
+        tools.push(tool);
+      }
+    }
+    return tools;
   }
 
   /**