fix: restore all CJS transform + env + event loop fixes. PI ESM error is balanced-match CJS interop. Both processes run.

Author: NathanFlurry

packages/nodejs/src/execution-driver.ts

@@ -902,7 +902,7 @@ export class NodeExecutionDriver implements RuntimeDriver {
 	}
 
 	private async waitForManagedResources(): Promise<void> {
-		const graceDeadline = Date.now() + 100;
+		const graceDeadline = Date.now() + 5000;
 
 		// Give async bridge callbacks a moment to register their host-side handles.
 		while (!this.disposed && !this.hasManagedResources() && Date.now() < graceDeadline) {
@@ -1048,8 +1048,12 @@ export class NodeExecutionDriver implements RuntimeDriver {
 		// large dependency trees (e.g., PI has hundreds of @sinclair/typebox
 		// sub-modules). CJS mode uses the in-process require-setup transform
 		// which is orders of magnitude faster.
-		const sessionMode = options.mode === "run" || entryIsEsm ? "run" : "exec";
-		const userCode = entryIsEsm
+		// If the code was already CJS-transformed by _resolveEntry (has the
+		// require-esm marker), use exec mode so require() and __dirname work.
+		const REQUIRE_ESM_MARKER = "/*__secure_exec_require_esm__*/";
+		const alreadyTransformed = options.code.startsWith(REQUIRE_ESM_MARKER);
+		const sessionMode = alreadyTransformed ? "exec" : (options.mode === "run" || entryIsEsm ? "run" : "exec");
+		const userCode = entryIsEsm && !alreadyTransformed
 			? options.code
 			: (() => {
 					const transformed = transformSourceForRequireSync(
@@ -1276,7 +1280,7 @@ export class NodeExecutionDriver implements RuntimeDriver {
 				},
 				timingMitigation,
 				frozenTimeMs,
-				options.mode,
+				sessionMode,
 				options.filePath,
 				bindingKeys,
 			);
@@ -1285,6 +1289,7 @@ export class NodeExecutionDriver implements RuntimeDriver {
 			this._currentSession = session;
 
 			// Execute in V8 session
+			console.error(`[exec] mode=${sessionMode} alreadyTransformed=${alreadyTransformed} entryIsEsm=${entryIsEsm} filePath=${options.filePath} codeLen=${userCode.length}`);
 			const result = await session.execute({
 				bridgeCode,
 				postRestoreScript,
@@ -1325,7 +1330,7 @@ export class NodeExecutionDriver implements RuntimeDriver {
 				},
 			});
 
-			if (options.mode === "exec" && !result.error) {
+			if (!result.error) {
 				await this.waitForManagedResources();
 			}
 
@@ -1537,7 +1542,9 @@ function buildPostRestoreScript(
 		parts.push(getIsolateRuntimeSource("applyTimingMitigationOff"));
 	}
 
-	// Apply env/cwd overrides for all modes (needed for ESM process.env access)
+	// Apply env, cwd, and stdin overrides for all modes.
+	// These must run even in "run" (ESM) mode so that process.env and
+	// process.cwd() reflect the spawn-time configuration.
 	if (processConfig.env) {
 		parts.push(`globalThis.__runtimeProcessEnvOverride = ${JSON.stringify(processConfig.env)};`);
 		parts.push(getIsolateRuntimeSource("overrideProcessEnv"));
@@ -1546,7 +1553,8 @@ function buildPostRestoreScript(
 		parts.push(`globalThis.__runtimeProcessCwdOverride = ${JSON.stringify(processConfig.cwd)};`);
 		parts.push(getIsolateRuntimeSource("overrideProcessCwd"));
 	}
-	// CJS file globals and stdin only for exec mode
+
+	// CJS file globals (__filename, __dirname, module) only for exec mode.
 	if (mode === "exec") {
 		const commonJsFileConfig = (() => {
 			if (filePath) {

packages/nodejs/src/kernel-runtime.ts

@@ -900,6 +900,21 @@ class NodeRuntimeDriver implements RuntimeDriver {
           if (hostPath) {
             try {
               const content = readFileSync(hostPath, 'utf-8');
+              // Check if this is an ESM module. V8's native ESM resolver is too slow
+              // for large dep trees due to per-module IPC. For overlay ESM scripts
+              // where the CJS transform succeeds, return transformed CJS code instead.
+              if (this._isOverlayEsmEntry(hostPath)) {
+                const transformed = transformSourceForRequireSync(content, scriptPath);
+                const REQUIRE_ESM_MARKER = "/*__secure_exec_require_esm__*/";
+                if (transformed.startsWith(REQUIRE_ESM_MARKER)) {
+                  console.error(`[_resolveEntry] ESM→CJS transform OK: ${scriptPath} (${content.length}→${transformed.length})`);
+                  return { code: transformed, filePath: scriptPath };
+                }
+                // CJS transform failed (e.g., top-level await). Fall through to
+                // V8 native ESM "run" mode. The V8 runtime pumps the event loop
+                // after module evaluation so timers and callbacks fire.
+                console.error(`[_resolveEntry] ESM→CJS failed, using V8 ESM run mode: ${scriptPath}`);
+              }
               return { code: content, filePath: scriptPath };
             } catch {
               // Fall through to the error below
@@ -913,4 +928,25 @@ class NodeRuntimeDriver implements RuntimeDriver {
     // No script or -e flag — read from stdin (not supported yet)
     throw new Error('node: missing script argument (stdin mode not supported)');
   }
+
+  /**
+   * Check if a host filesystem path points to an ESM module by reading
+   * the nearest package.json for "type": "module". Used to decide whether
+   * to wrap overlay entry scripts in a CJS require() call.
+   */
+  private _isOverlayEsmEntry(hostPath: string): boolean {
+    let dir = dirname(hostPath);
+    for (let i = 0; i < 10; i++) {
+      const pkgJsonPath = join(dir, 'package.json');
+      try {
+        const pkg = JSON.parse(readFileSync(pkgJsonPath, 'utf-8'));
+        return pkg.type === 'module';
+      } catch {
+        const parent = dirname(dir);
+        if (parent === dir) break;
+        dir = parent;
+      }
+    }
+    return false;
+  }
 }