[UPDATE PRIMITIVE] Fix ZodEffects schema rejection in CLI tool registration and resolve_queries parameter name (#225)

* fix: use registerTool() instead of deprecated tool() to fix ZodEffects schema rejection by MCP SDK

The MCP SDK's tool() method argument parsing rejects ZodEffects schemas
(from buildEnhancedToolSchema) as 'unrecognized objects' because its
isZodRawShapeCompat() check returns false for Zod schema instances.

registerTool() passes inputSchema directly to getZodSchemaObject(),
which correctly recognises any Zod schema instance, avoiding the error:
'Tool codeql_bqrs_decode expected a Zod schema or ToolAnnotations,
but received an unrecognized object'

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/ba14c9e0-173d-49fd-820b-b77bfdd973b0

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

* fix: use correct parameter name 'directory' instead of 'path' for codeql_resolve_queries integration test

The codeql_resolve_queries tool schema defines 'directory' as the parameter
for specifying the directory to search for queries, but the integration test
runner was sending 'path' which was rejected as an unknown property by the
parameter normalization layer.

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/ba14c9e0-173d-49fd-820b-b77bfdd973b0

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Author: Copilot

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

@@ -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[] = [];