fix(coding-agent): reserve stdout in print and json mode closes #2482

packages/coding-agent/CHANGELOG.md

@@ -14,6 +14,7 @@
 ### Fixed
 
 - Fixed `pi update` for git packages to skip destructive reset, clean, and reinstall steps when the fetched target already matches the local checkout ([#2503](https://github.com/badlogic/pi-mono/issues/2503))
+- Fixed print and JSON mode to take over stdout during non-interactive startup, keeping package-manager and other incidental chatter off protocol/output stdout ([#2482](https://github.com/badlogic/pi-mono/issues/2482))
 
 ## [0.61.1] - 2026-03-20
 

packages/coding-agent/src/core/output-guard.ts

@@ -0,0 +1,74 @@
+interface StdoutTakeoverState {
+	rawStdoutWrite: (chunk: string, callback?: (error?: Error | null) => void) => boolean;
+	rawStderrWrite: (chunk: string, callback?: (error?: Error | null) => void) => boolean;
+	originalStdoutWrite: typeof process.stdout.write;
+}
+
+let stdoutTakeoverState: StdoutTakeoverState | undefined;
+
+export function takeOverStdout(): void {
+	if (stdoutTakeoverState) {
+		return;
+	}
+
+	const rawStdoutWrite = process.stdout.write.bind(process.stdout) as StdoutTakeoverState["rawStdoutWrite"];
+	const rawStderrWrite = process.stderr.write.bind(process.stderr) as StdoutTakeoverState["rawStderrWrite"];
+	const originalStdoutWrite = process.stdout.write;
+
+	process.stdout.write = ((
+		chunk: string | Uint8Array,
+		encodingOrCallback?: BufferEncoding | ((error?: Error | null) => void),
+		callback?: (error?: Error | null) => void,
+	): boolean => {
+		if (typeof encodingOrCallback === "function") {
+			return rawStderrWrite(String(chunk), encodingOrCallback);
+		}
+		return rawStderrWrite(String(chunk), callback);
+	}) as typeof process.stdout.write;
+
+	stdoutTakeoverState = {
+		rawStdoutWrite,
+		rawStderrWrite,
+		originalStdoutWrite,
+	};
+}
+
+export function restoreStdout(): void {
+	if (!stdoutTakeoverState) {
+		return;
+	}
+
+	process.stdout.write = stdoutTakeoverState.originalStdoutWrite;
+	stdoutTakeoverState = undefined;
+}
+
+export function isStdoutTakenOver(): boolean {
+	return stdoutTakeoverState !== undefined;
+}
+
+export function writeRawStdout(text: string): void {
+	if (stdoutTakeoverState) {
+		stdoutTakeoverState.rawStdoutWrite(text);
+		return;
+	}
+	process.stdout.write(text);
+}
+
+export async function flushRawStdout(): Promise<void> {
+	if (stdoutTakeoverState) {
+		await new Promise<void>((resolve, reject) => {
+			stdoutTakeoverState?.rawStdoutWrite("", (err) => {
+				if (err) reject(err);
+				else resolve();
+			});
+		});
+		return;
+	}
+
+	await new Promise<void>((resolve, reject) => {
+		process.stdout.write("", (err) => {
+			if (err) reject(err);
+			else resolve();
+		});
+	});
+}

packages/coding-agent/src/core/package-manager.ts

@@ -7,6 +7,7 @@ import ignore from "ignore";
 import { minimatch } from "minimatch";
 import { CONFIG_DIR_NAME } from "../config.js";
 import { type GitSource, parseGitUrl } from "../utils/git.js";
+import { isStdoutTakenOver } from "./output-guard.js";
 import type { PackageSource, SettingsManager } from "./settings-manager.js";
 
 const NETWORK_TIMEOUT_MS = 10000;
@@ -2091,7 +2092,7 @@ export class DefaultPackageManager implements PackageManager {
 		return new Promise((resolvePromise, reject) => {
 			const child = spawn(command, args, {
 				cwd: options?.cwd,
-				stdio: "inherit",
+				stdio: isStdoutTakenOver() ? ["ignore", 2, 2] : "inherit",
 				shell: process.platform === "win32",
 			});
 			child.on("error", reject);

packages/coding-agent/src/main.ts

@@ -21,6 +21,7 @@ import type { LoadExtensionsResult } from "./core/extensions/index.js";
 import { migrateKeybindingsConfigFile } from "./core/keybindings.js";
 import { ModelRegistry } from "./core/model-registry.js";
 import { resolveCliModel, resolveModelScope, type ScopedModel } from "./core/model-resolver.js";
+import { restoreStdout, takeOverStdout } from "./core/output-guard.js";
 import { DefaultPackageManager } from "./core/package-manager.js";
 import { DefaultResourceLoader } from "./core/resource-loader.js";
 import { type CreateAgentSessionOptions, createAgentSession } from "./core/sdk.js";
@@ -635,11 +636,15 @@ export async function main(args: string[]) {
 		return;
 	}
 
-	// Run migrations (pass cwd for project-local migrations)
-	const { migratedAuthProviders: migratedProviders, deprecationWarnings } = runMigrations(process.cwd());
-
 	// First pass: parse args to get --extension paths
 	const firstPass = parseArgs(args);
+	const shouldTakeOverStdout = firstPass.mode !== undefined || firstPass.print || !process.stdin.isTTY;
+	if (shouldTakeOverStdout) {
+		takeOverStdout();
+	}
+
+	// Run migrations (pass cwd for project-local migrations)
+	const { migratedAuthProviders: migratedProviders, deprecationWarnings } = runMigrations(process.cwd());
 
 	// Early load extensions to discover their CLI flags
 	const cwd = process.cwd();
@@ -884,9 +889,7 @@ export async function main(args: string[]) {
 			initialImages,
 		});
 		stopThemeWatcher();
-		if (process.stdout.writableLength > 0) {
-			await new Promise<void>((resolve) => process.stdout.once("drain", resolve));
-		}
-		process.exit(0);
+		restoreStdout();
+		return;
 	}
 }

packages/coding-agent/src/modes/print-mode.ts

@@ -8,6 +8,7 @@
 
 import type { AssistantMessage, ImageContent } from "@mariozechner/pi-ai";
 import type { AgentSession } from "../core/agent-session.js";
+import { flushRawStdout, writeRawStdout } from "../core/output-guard.js";
 
 /**
  * Options for print mode.
@@ -32,7 +33,7 @@ export async function runPrintMode(session: AgentSession, options: PrintModeOpti
 	if (mode === "json") {
 		const header = session.sessionManager.getHeader();
 		if (header) {
-			console.log(JSON.stringify(header));
+			writeRawStdout(`${JSON.stringify(header)}\n`);
 		}
 	}
 	// Set up extensions for print mode (no UI)
@@ -76,7 +77,7 @@ export async function runPrintMode(session: AgentSession, options: PrintModeOpti
 	session.subscribe((event) => {
 		// In JSON mode, output all events
 		if (mode === "json") {
-			console.log(JSON.stringify(event));
+			writeRawStdout(`${JSON.stringify(event)}\n`);
 		}
 	});
 
@@ -107,7 +108,7 @@ export async function runPrintMode(session: AgentSession, options: PrintModeOpti
 			// Output text content
 			for (const content of assistantMsg.content) {
 				if (content.type === "text") {
-					console.log(content.text);
+					writeRawStdout(`${content.text}\n`);
 				}
 			}
 		}
@@ -115,10 +116,5 @@ export async function runPrintMode(session: AgentSession, options: PrintModeOpti
 
 	// Ensure stdout is fully flushed before returning
 	// This prevents race conditions where the process exits before all output is written
-	await new Promise<void>((resolve, reject) => {
-		process.stdout.write("", (err) => {
-			if (err) reject(err);
-			else resolve();
-		});
-	});
+	await flushRawStdout();
 }

packages/coding-agent/src/modes/rpc/rpc-mode.ts

@@ -18,6 +18,7 @@ import type {
 	ExtensionUIDialogOptions,
 	ExtensionWidgetOptions,
 } from "../../core/extensions/index.js";
+import { takeOverStdout, writeRawStdout } from "../../core/output-guard.js";
 import { type Theme, theme } from "../interactive/theme/theme.js";
 import { attachJsonlLineReader, serializeJsonLine } from "./jsonl.js";
 import type {
@@ -43,15 +44,10 @@ export type {
  * Listens for JSON commands on stdin, outputs events and responses on stdout.
  */
 export async function runRpcMode(session: AgentSession): Promise<never> {
-	const rawStdoutWrite = process.stdout.write.bind(process.stdout);
-	const rawStderrWrite = process.stderr.write.bind(process.stderr);
-
-	process.stdout.write = ((
-		...args: Parameters<typeof process.stdout.write>
-	): ReturnType<typeof process.stdout.write> => rawStderrWrite(...args)) as typeof process.stdout.write;
+	takeOverStdout();
 
 	const output = (obj: RpcResponse | RpcExtensionUIRequest | object) => {
-		rawStdoutWrite(serializeJsonLine(obj));
+		writeRawStdout(serializeJsonLine(obj));
 	};
 
 	const success = <T extends RpcCommand["type"]>(

packages/coding-agent/test/stdout-cleanliness.test.ts

@@ -0,0 +1,102 @@
+import { spawn } from "node:child_process";
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join, resolve } from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import { ENV_AGENT_DIR } from "../src/config.js";
+
+const cliPath = resolve(__dirname, "../src/cli.ts");
+const tsxPath = resolve(__dirname, "../../../node_modules/tsx/dist/cli.mjs");
+
+const tempDirs: string[] = [];
+
+afterEach(() => {
+	for (const dir of tempDirs.splice(0)) {
+		rmSync(dir, { recursive: true, force: true });
+	}
+});
+
+function createTempDir(): string {
+	const dir = mkdtempSync(join(tmpdir(), "pi-stdout-clean-"));
+	tempDirs.push(dir);
+	return dir;
+}
+
+async function runCli(args: string[]): Promise<{ stdout: string; stderr: string; code: number | null }> {
+	const tempRoot = createTempDir();
+	const agentDir = join(tempRoot, "agent");
+	const projectDir = join(tempRoot, "project");
+	const projectConfigDir = join(projectDir, ".pi");
+	mkdirSync(agentDir, { recursive: true });
+	mkdirSync(projectConfigDir, { recursive: true });
+
+	const fakeNpmPath = join(tempRoot, "fake-npm.mjs");
+	writeFileSync(
+		fakeNpmPath,
+		[
+			'console.log("changed 1 package in 471ms");',
+			'console.log("found 0 vulnerabilities");',
+			"process.exit(0);",
+		].join("\n"),
+		"utf-8",
+	);
+
+	writeFileSync(
+		join(projectConfigDir, "settings.json"),
+		JSON.stringify(
+			{
+				packages: ["npm:fake-package"],
+				npmCommand: [process.execPath, fakeNpmPath],
+			},
+			null,
+			2,
+		),
+		"utf-8",
+	);
+
+	return await new Promise((resolvePromise, reject) => {
+		const child = spawn(process.execPath, [tsxPath, cliPath, ...args], {
+			cwd: projectDir,
+			env: {
+				...process.env,
+				[ENV_AGENT_DIR]: agentDir,
+			},
+			stdio: ["ignore", "pipe", "pipe"],
+		});
+
+		let stdout = "";
+		let stderr = "";
+		child.stdout.on("data", (chunk) => {
+			stdout += chunk.toString();
+		});
+		child.stderr.on("data", (chunk) => {
+			stderr += chunk.toString();
+		});
+		child.on("error", reject);
+		child.on("close", (code) => {
+			resolvePromise({ stdout, stderr, code });
+		});
+	});
+}
+
+describe("stdout cleanliness in non-interactive modes", () => {
+	it("keeps stdout empty for --mode json --help while routing startup chatter to stderr", async () => {
+		const result = await runCli(["--mode", "json", "--help"]);
+
+		expect(result.code).toBe(0);
+		expect(result.stdout).toBe("");
+		expect(result.stderr).toContain("changed 1 package in 471ms");
+		expect(result.stderr).toContain("found 0 vulnerabilities");
+		expect(result.stderr).toContain("Usage:");
+	});
+
+	it("keeps stdout empty for -p --help while routing startup chatter to stderr", async () => {
+		const result = await runCli(["-p", "--help"]);
+
+		expect(result.code).toBe(0);
+		expect(result.stdout).toBe("");
+		expect(result.stderr).toContain("changed 1 package in 471ms");
+		expect(result.stderr).toContain("found 0 vulnerabilities");
+		expect(result.stderr).toContain("Usage:");
+	});
+});