[UPDATE PRIMITIVE] Fix ZodEffects schema rejection in CLI tool registration and resolve_queries parameter name

client/src/lib/integration-test-runner.js

@@ -1084,8 +1084,8 @@ export class IntegrationTestRunner {
         throw new Error(`Test directory ${beforeDir} not found for ${toolName}/${testCase}`);
       }
     } else if (toolName === "codeql_resolve_queries") {
-      // Use the test case directory as the queries path
-      params.path = beforeDir;
+      // Use the static examples directory which already contains installed QL packs
+      params.directory = path.join(staticPath, "src");
     } else if (toolName === "codeql_resolve_tests") {
       // Use the test case directory as the tests path
       params.tests = [beforeDir];

server/dist/codeql-development-mcp-server.js

@@ -193542,13 +193542,17 @@ function registerCLITool(server, definition) {
     resultProcessor = defaultCLIResultProcessor
   } = definition;
   const enhancedSchema = buildEnhancedToolSchema(inputSchema);
-  server.tool(
+  server.registerTool(
     name,
-    description,
-    // The enhanced schema is a pre-built ZodEffects (passthrough + transform).
-    // The MCP SDK's getZodSchemaObject() detects it as a Zod schema instance
-    // and passes it through without re-wrapping.
-    enhancedSchema,
+    {
+      description,
+      // The enhanced schema is a pre-built ZodEffects (passthrough + transform).
+      // Using registerTool() instead of tool() because the latter's argument
+      // parsing rejects ZodEffects as "unrecognized objects".  registerTool()
+      // passes inputSchema directly to getZodSchemaObject(), which correctly
+      // recognises any Zod schema instance.
+      inputSchema: enhancedSchema
+    },
     async (params) => {
       const tempDirsToCleanup = [];
       try {

server/src/lib/cli-tool-registry.ts

@@ -115,13 +115,17 @@ export function registerCLITool(server: McpServer, definition: CLIToolDefinition
   // produces actionable error messages for truly unknown keys.
   const enhancedSchema = buildEnhancedToolSchema(inputSchema);
 
-  server.tool(
+  server.registerTool(
     name,
-    description,
-    // The enhanced schema is a pre-built ZodEffects (passthrough + transform).
-    // The MCP SDK's getZodSchemaObject() detects it as a Zod schema instance
-    // and passes it through without re-wrapping.
-    enhancedSchema as unknown as Record<string, z.ZodTypeAny>,
+    {
+      description,
+      // The enhanced schema is a pre-built ZodEffects (passthrough + transform).
+      // Using registerTool() instead of tool() because the latter's argument
+      // parsing rejects ZodEffects as "unrecognized objects".  registerTool()
+      // passes inputSchema directly to getZodSchemaObject(), which correctly
+      // recognises any Zod schema instance.
+      inputSchema: enhancedSchema,
+    },
     async (params: Record<string, unknown>) => {
       // Track temporary directories for cleanup
       const tempDirsToCleanup: string[] = [];