fix bugs in stdio MCP client

Bug 1 — CWD mismatch in stdio mode (both platforms):
StdioClientTransport inherited the client/ working directory, so
relative paths passed to CodeQL CLI (e.g. server/ql/javascript/...)
resolved to client/server/ql/... which does not exist. Add cwd: repoRoot
to the transport options to match the HTTP-mode behavior where
start-server.sh explicitly cd's to the repo root.

Bug 2 — False success on Windows in stdio mode:
StdioClientTransport.close() could cause an abrupt process exit on
Windows before printTestSummary() and process.exit(exitCode) were
reached, so the shell script saw exit code 0 and reported success
despite test failures. Move summary printing and process.exitCode
assignment above the disconnect() call in all four run methods so
results are always reported even if disconnect triggers an early exit.

Author: data-douser

client/integration-tests/primitives/tools/codeql_bqrs_interpret/sarif_format/after/results.sarif

@@ -1 +1 @@
-{"$schema":"https://json.schemastore.org/sarif-2.1.0.json","version":"2.1.0","runs":[{"tool":{"driver":{"name":"CodeQL","organization":"GitHub","semanticVersion":"2.24.1","rules":[{"id":"test/query","name":"test/query","shortDescription":{"text":"ExampleQuery1"},"fullDescription":{"text":"Example query for integration testing of the codeql_test_extract MCP server tool."},"defaultConfiguration":{"enabled":true,"level":"warning"},"help":{"text":"# Query Help for JavaScript ExampleQuery1\n\nTODO\n","markdown":"# Query Help for JavaScript ExampleQuery1\n\nTODO\n"},"properties":{"tags":["mcp-integration-tests"],"description":"Example query for integration testing of the codeql_test_extract MCP server tool.","id":"test/query","kind":"problem","name":"ExampleQuery1","precision":"medium","problem.severity":"warning"}}]},"extensions":[{"name":"mcp-client-integration-tests-static-javascript-src","semanticVersion":"0.0.1+fe0e7d2a7059ebb6c6075ff8eaea04f382747656","locations":[{"uri":"file:///home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/src/","description":{"text":"The QL pack root directory."},"properties":{"tags":["CodeQL/LocalPackRoot"]}},{"uri":"file:///home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/src/codeql-pack.yml","description":{"text":"The QL pack definition file."},"properties":{"tags":["CodeQL/LocalPackDefinitionFile"]}}]},{"name":"codeql/javascript-all","semanticVersion":"2.6.11+ce9c8e6e9fd41ef0967b13849bb6ae2183caf9ad","locations":[{"uri":"file:///home/runner/.codeql/packages/codeql/javascript-all/2.6.11/","description":{"text":"The QL pack root directory."},"properties":{"tags":["CodeQL/LocalPackRoot"]}},{"uri":"file:///home/runner/.codeql/packages/codeql/javascript-all/2.6.11/qlpack.yml","description":{"text":"The QL pack definition file."},"properties":{"tags":["CodeQL/LocalPackDefinitionFile"]}}]},{"name":"codeql/threat-models","semanticVersion":"1.0.31+ce9c8e6e9fd41ef0967b13849bb6ae2183caf9ad","locations":[{"uri":"file:///home/runner/.codeql/packages/codeql/threat-models/1.0.31/","description":{"text":"The QL pack root directory."},"properties":{"tags":["CodeQL/LocalPackRoot"]}},{"uri":"file:///home/runner/.codeql/packages/codeql/threat-models/1.0.31/qlpack.yml","description":{"text":"The QL pack definition file."},"properties":{"tags":["CodeQL/LocalPackDefinitionFile"]}}]}]},"artifacts":[{"location":{"uri":"file:/home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/test/ExampleQuery1/ExampleQuery1.js","index":0}}],"results":[{"ruleId":"test/query","ruleIndex":0,"rule":{"id":"test/query","index":0},"message":{"text":"Example test code file found for codeql_test_extract example query."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"file:/home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/test/ExampleQuery1/ExampleQuery1.js","index":0}}}]}],"columnKind":"utf16CodeUnits","properties":{"semmle.formatSpecifier":"sarif-latest"}}]}
+{"$schema":"https://json.schemastore.org/sarif-2.1.0.json","version":"2.1.0","runs":[{"tool":{"driver":{"name":"CodeQL","organization":"GitHub","semanticVersion":"2.24.2","rules":[{"id":"test/query","name":"test/query","shortDescription":{"text":"ExampleQuery1"},"fullDescription":{"text":"Example query for integration testing of the codeql_test_extract MCP server tool."},"defaultConfiguration":{"enabled":true,"level":"warning"},"help":{"text":"# Query Help for JavaScript ExampleQuery1\n\nTODO\n","markdown":"# Query Help for JavaScript ExampleQuery1\n\nTODO\n"},"properties":{"tags":["mcp-integration-tests"],"description":"Example query for integration testing of the codeql_test_extract MCP server tool.","id":"test/query","kind":"problem","name":"ExampleQuery1","precision":"medium","problem.severity":"warning"}}]},"extensions":[{"name":"mcp-client-integration-tests-static-javascript-src","semanticVersion":"0.0.1+fe0e7d2a7059ebb6c6075ff8eaea04f382747656","locations":[{"uri":"file:///home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/src/","description":{"text":"The QL pack root directory."},"properties":{"tags":["CodeQL/LocalPackRoot"]}},{"uri":"file:///home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/src/codeql-pack.yml","description":{"text":"The QL pack definition file."},"properties":{"tags":["CodeQL/LocalPackDefinitionFile"]}}]},{"name":"codeql/javascript-all","semanticVersion":"2.6.11+ce9c8e6e9fd41ef0967b13849bb6ae2183caf9ad","locations":[{"uri":"file:///home/runner/.codeql/packages/codeql/javascript-all/2.6.11/","description":{"text":"The QL pack root directory."},"properties":{"tags":["CodeQL/LocalPackRoot"]}},{"uri":"file:///home/runner/.codeql/packages/codeql/javascript-all/2.6.11/qlpack.yml","description":{"text":"The QL pack definition file."},"properties":{"tags":["CodeQL/LocalPackDefinitionFile"]}}]},{"name":"codeql/threat-models","semanticVersion":"1.0.31+ce9c8e6e9fd41ef0967b13849bb6ae2183caf9ad","locations":[{"uri":"file:///home/runner/.codeql/packages/codeql/threat-models/1.0.31/","description":{"text":"The QL pack root directory."},"properties":{"tags":["CodeQL/LocalPackRoot"]}},{"uri":"file:///home/runner/.codeql/packages/codeql/threat-models/1.0.31/qlpack.yml","description":{"text":"The QL pack definition file."},"properties":{"tags":["CodeQL/LocalPackDefinitionFile"]}}]}]},"artifacts":[{"location":{"uri":"file:///home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/test/ExampleQuery1/ExampleQuery1.js","index":0}}],"results":[{"ruleId":"test/query","ruleIndex":0,"rule":{"id":"test/query","index":0},"message":{"text":"Example test code file found for codeql_test_extract example query."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"file:///home/runner/work/codeql-development-mcp-server/codeql-development-mcp-server/client/integration-tests/static/javascript/test/ExampleQuery1/ExampleQuery1.js","index":0}}}]}],"columnKind":"utf16CodeUnits","properties":{"semmle.formatSpecifier":"sarif-latest"}}]}

client/src/ql-mcp-client.js

@@ -123,12 +123,14 @@ class CodeQLMCPClient {
       });
 
       if (this.mcpMode === "stdio") {
+        const repoRoot = path.join(__dirname, "..", "..");
         const serverPath =
           process.env.MCP_SERVER_PATH ||
-          path.join(__dirname, "..", "..", "server", "dist", "codeql-development-mcp-server.js");
+          path.join(repoRoot, "server", "dist", "codeql-development-mcp-server.js");
         this.transport = new StdioClientTransport({
           command: "node",
           args: [serverPath],
+          cwd: repoRoot,
           env: {
             ...process.env,
             TRANSPORT_MODE: "stdio"
@@ -215,17 +217,24 @@ class CodeQLMCPClient {
       }
     } catch (error) {
       this.logger.log(`Test execution failed: ${error.message}`, "ERROR");
-    } finally {
-      if (connected) {
-        await this.disconnect();
-      }
     }
 
-    // Print test summary
+    // Print test summary and set exit code BEFORE disconnect.
+    // On Windows, StdioClientTransport.close() can cause the Node.js
+    // process to exit abruptly, so we must report results first.
     this.logger.printTestSummary();
+    const exitCode = this.logger.isSuccess() ? 0 : 1;
+    process.exitCode = exitCode;
+
+    if (connected) {
+      try {
+        await this.disconnect();
+      } catch {
+        // Ignore disconnect errors — results are already reported
+      }
+    }
 
-    // Exit with appropriate code
-    process.exit(this.logger.isSuccess() ? 0 : 1);
+    process.exit(exitCode);
   }
 
   /**
@@ -246,17 +255,24 @@ class CodeQLMCPClient {
       }
     } catch (error) {
       this.logger.log(`Demo execution failed: ${error.message}`, "ERROR");
-    } finally {
-      if (connected) {
-        await this.disconnect();
-      }
     }
 
-    // Print demo summary
+    // Print summary and set exit code BEFORE disconnect.
+    // On Windows, StdioClientTransport.close() can cause the Node.js
+    // process to exit abruptly, so we must report results first.
     this.logger.printTestSummary();
+    const exitCode = this.logger.isSuccess() ? 0 : 1;
+    process.exitCode = exitCode;
+
+    if (connected) {
+      try {
+        await this.disconnect();
+      } catch {
+        // Ignore disconnect errors — results are already reported
+      }
+    }
 
-    // Exit with appropriate code
-    process.exit(this.logger.isSuccess() ? 0 : 1);
+    process.exit(exitCode);
   }
 
   /**
@@ -350,17 +366,24 @@ class CodeQLMCPClient {
       }
     } catch (error) {
       this.logger.log(`Workflow test execution failed: ${error.message}`, "ERROR");
-    } finally {
-      if (connected) {
-        await this.disconnect();
-      }
     }
 
-    // Print test summary
+    // Print test summary and set exit code BEFORE disconnect.
+    // On Windows, StdioClientTransport.close() can cause the Node.js
+    // process to exit abruptly, so we must report results first.
     this.logger.printTestSummary();
+    const exitCode = this.logger.isSuccess() ? 0 : 1;
+    process.exitCode = exitCode;
+
+    if (connected) {
+      try {
+        await this.disconnect();
+      } catch {
+        // Ignore disconnect errors — results are already reported
+      }
+    }
 
-    // Exit with appropriate code
-    process.exit(this.logger.isSuccess() ? 0 : 1);
+    process.exit(exitCode);
   }
 
   /**
@@ -387,17 +410,24 @@ class CodeQLMCPClient {
       }
     } catch (error) {
       this.logger.log(`Monitoring test execution failed: ${error.message}`, "ERROR");
-    } finally {
-      if (connected) {
-        await this.disconnect();
-      }
     }
 
-    // Print test summary
+    // Print test summary and set exit code BEFORE disconnect.
+    // On Windows, StdioClientTransport.close() can cause the Node.js
+    // process to exit abruptly, so we must report results first.
     this.logger.printTestSummary();
+    const exitCode = this.logger.isSuccess() ? 0 : 1;
+    process.exitCode = exitCode;
+
+    if (connected) {
+      try {
+        await this.disconnect();
+      } catch {
+        // Ignore disconnect errors — results are already reported
+      }
+    }
 
-    // Exit with appropriate code
-    process.exit(this.logger.isSuccess() ? 0 : 1);
+    process.exit(exitCode);
   }
 
   /**