diff --git a/packages/coding-agent/npm-shrinkwrap.json b/packages/coding-agent/npm-shrinkwrap.json
index bb4be5bcc..a50b306c8 100644
--- a/packages/coding-agent/npm-shrinkwrap.json
+++ b/packages/coding-agent/npm-shrinkwrap.json
@@ -486,7 +486,7 @@
 		},
 		"node_modules/@earendil-works/pi-agent-core": {
 			"version": "2026.5.29-4",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-agent-core/-/pi-agent-core-2026.5.29-4.tgz",
+			"inBundle": true,
 			"license": "MIT",
 			"dependencies": {
 				"@earendil-works/pi-ai": "^2026.5.29-4",
@@ -500,7 +500,7 @@
 		},
 		"node_modules/@earendil-works/pi-ai": {
 			"version": "2026.5.29-4",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-ai/-/pi-ai-2026.5.29-4.tgz",
+			"inBundle": true,
 			"license": "MIT",
 			"dependencies": {
 				"@anthropic-ai/sdk": "0.91.1",
@@ -527,7 +527,7 @@
 		},
 		"node_modules/@earendil-works/pi-tui": {
 			"version": "2026.5.29-4",
-			"resolved": "https://registry.npmjs.org/@earendil-works/pi-tui/-/pi-tui-2026.5.29-4.tgz",
+			"inBundle": true,
 			"license": "MIT",
 			"dependencies": {
 				"get-east-asian-width": "1.6.0",
diff --git a/scripts/build-all.mjs b/scripts/build-all.mjs
index 985438424..aafbbb093 100644
--- a/scripts/build-all.mjs
+++ b/scripts/build-all.mjs
@@ -91,10 +91,10 @@ export function cleanEnv(envSource = process.env) {
 function spawnPmAsync(pm, args, cwd, env) {
 	// bun's execpath is a native binary so we invoke it directly.
 	// npm's and pnpm's execpaths are .js / .cjs entry points that have to
-	// be loaded through the current Node runtime.
+	// be loaded through the current Node runtime, unless they are native binaries (like pnpm.exe).
 	let command = pm.cmd;
 	let spawnArgs = args;
-	if (pm.execpath && pm.cmd === "bun") {
+	if (pm.execpath && (pm.cmd === "bun" || !/\.[cm]?js$/i.test(pm.execpath))) {
 		command = pm.execpath;
 	} else if (pm.execpath) {
 		command = process.execPath;
diff --git a/scripts/generate-coding-agent-shrinkwrap.mjs b/scripts/generate-coding-agent-shrinkwrap.mjs
index 7bcf56813..7c8a3962a 100644
--- a/scripts/generate-coding-agent-shrinkwrap.mjs
+++ b/scripts/generate-coding-agent-shrinkwrap.mjs
@@ -46,6 +46,7 @@ function sortedPackageEntry(entry) {
 		"version",
 		"resolved",
 		"integrity",
+		"inBundle",
 		"license",
 		"dependencies",
 		"optionalDependencies",
@@ -196,7 +197,7 @@ function addInternalWorkspace(shrinkwrapPackages, addedPaths, queue, name, works
 	const packageJson = workspace.packageJson;
 	const outputPath = `node_modules/${name}`;
 	const entry = copyPackageJsonEntry(packageJson, { includeName: false });
-	entry.resolved = registryTarballUrl(name, packageJson.version);
+	entry.inBundle = true;
 
 	shrinkwrapPackages[outputPath] = sortedPackageEntry(entry);
 	addedPaths.add(outputPath);
diff --git a/scripts/run-web-ui-check.mjs b/scripts/run-web-ui-check.mjs
index 4938a3798..e813ff858 100644
--- a/scripts/run-web-ui-check.mjs
+++ b/scripts/run-web-ui-check.mjs
@@ -38,9 +38,9 @@ function detectPm() {
 }
 
 const pm = detectPm();
-// bun's execpath is a native binary, npm/pnpm are .js we load via Node.
+// bun's execpath is a native binary, npm/pnpm are .js we load via Node, unless they are native binaries (like pnpm.exe).
 function runCheck() {
-	if (pm.execpath && pm.cmd === "bun") {
+	if (pm.execpath && (pm.cmd === "bun" || !/\.[cm]?js$/i.test(pm.execpath))) {
 		return spawnSync(pm.execpath, ["run", "check"], { cwd: webUiDir, stdio: "inherit", env, shell: false });
 	}
 	if (pm.execpath) {