diff --git a/packages/coding-agent/src/session/session-manager.ts b/packages/coding-agent/src/session/session-manager.ts
index 4b07c74c3..e3d8018e1 100644
--- a/packages/coding-agent/src/session/session-manager.ts
+++ b/packages/coding-agent/src/session/session-manager.ts
@@ -1334,6 +1334,18 @@ export class SessionManager {
 		return [...this.#additionalDirectories];
 	}
 
+	/**
+	 * Persist a workspace-directory change to the session header. Respects the
+	 * lazy-persistence gate: a session with no durable output yet keeps the
+	 * change in memory (the header lands with the first real write), so seeding
+	 * roots at launch never materializes an empty resumable session file.
+	 */
+	async #persistWorkspaceDirectoriesChange(): Promise<void> {
+		if (!this.#persist || !this.#sessionFile || !this.#shouldHaveSessionFile()) return;
+		this.#rewriteRequired = true;
+		await this.#rewriteAtomically();
+	}
+
 	/**
 	 * Add a workspace directory. Normalizes (relative to cwd), dedupes, rejects
 	 * the cwd itself, persists to the session header, and triggers an atomic
@@ -1348,10 +1360,7 @@ export class SessionManager {
 		if (this.#additionalDirectories.includes(resolved)) return null;
 		this.#additionalDirectories = [...this.#additionalDirectories, resolved];
 		this.#header.additionalDirectories = this.#additionalDirectories;
-		if (this.#persist && this.#sessionFile) {
-			this.#rewriteRequired = true;
-			await this.#rewriteAtomically();
-		}
+		await this.#persistWorkspaceDirectoriesChange();
 		return resolved;
 	}
 
@@ -1370,26 +1379,24 @@ export class SessionManager {
 		} else {
 			this.#header.additionalDirectories = this.#additionalDirectories;
 		}
-		if (this.#persist && this.#sessionFile) {
-			this.#rewriteRequired = true;
-			await this.#rewriteAtomically();
-		}
+		await this.#persistWorkspaceDirectoriesChange();
 		return resolved;
 	}
 
-	/** Seed additional directories from settings or a passed list. Also called on resumed sessions with --add-dir; persists the updated header when a session file already exists. */
+	/** Seed additional directories from settings or a passed list. Also called on resumed sessions with --add-dir; persists the updated header when the session file is already durable. No-op when the normalized list is unchanged (avoids rewriting large session files on every startup). */
 	async setAdditionalDirectories(directories: string[]): Promise<void> {
 		const workspace = normalizeSessionWorkspace({ cwd: this.#cwd, directories });
-		this.#additionalDirectories = additionalWorkspaceDirectories(workspace);
+		const next = additionalWorkspaceDirectories(workspace);
+		if (next.length === this.#additionalDirectories.length && next.every((d, i) => d === this.#additionalDirectories[i])) {
+			return;
+		}
+		this.#additionalDirectories = next;
 		if (this.#additionalDirectories.length > 0) {
 			this.#header.additionalDirectories = this.#additionalDirectories;
 		} else {
 			this.#header.additionalDirectories = undefined;
 		}
-		if (this.#persist && this.#sessionFile) {
-			this.#rewriteRequired = true;
-			await this.#rewriteAtomically();
-		}
+		await this.#persistWorkspaceDirectoriesChange();
 	}
 
 	getUsageStatistics(): UsageStatistics {
diff --git a/packages/coding-agent/test/session-manager/workspace-directories.test.ts b/packages/coding-agent/test/session-manager/workspace-directories.test.ts
index efc06bb52..34c40eda6 100644
--- a/packages/coding-agent/test/session-manager/workspace-directories.test.ts
+++ b/packages/coding-agent/test/session-manager/workspace-directories.test.ts
@@ -8,6 +8,7 @@ import {
 	normalizeSessionWorkspace,
 } from "@oh-my-pi/pi-coding-agent/session/session-workspace";
 import { TempDir } from "@oh-my-pi/pi-utils";
+import { makeAssistantMessage } from "./helpers";
 
 describe("normalizeSessionWorkspace", () => {
 	it("places cwd first and dedupes additional directories", () => {
@@ -105,8 +106,8 @@ describe("SessionManager workspace directories", () => {
 		using tempDir = TempDir.createSync("@pi-session-workspace-persist-");
 		const session = SessionManager.create(tempDir.path(), tempDir.path());
 		await session.addWorkspaceDirectory(path.join(tempDir.path(), "sibling"));
-		// Materialize on disk so reopen reads the header.
-		session.appendMessage({ role: "user", content: "hello", timestamp: 1 });
+		// Materialize on disk so reopen reads the header (lazy gate needs assistant output).
+		session.appendMessage(makeAssistantMessage());
 		await session.flush();
 
 		const file = session.getSessionFile();
@@ -123,7 +124,7 @@ describe("SessionManager workspace directories", () => {
 		using tempDir = TempDir.createSync("@pi-session-workspace-clear-");
 		const session = SessionManager.create(tempDir.path(), tempDir.path());
 		await session.addWorkspaceDirectory(path.join(tempDir.path(), "extra"));
-		session.appendMessage({ role: "user", content: "hi", timestamp: 1 });
+		session.appendMessage(makeAssistantMessage());
 		await session.flush();
 
 		await session.removeWorkspaceDirectory(path.join(tempDir.path(), "extra"));
@@ -149,8 +150,8 @@ describe("SessionManager workspace directories", () => {
 	it("setAdditionalDirectories persists the updated header on a resumed session", async () => {
 		using tempDir = TempDir.createSync("@pi-session-workspace-resume-");
 		const session = SessionManager.create(tempDir.path(), tempDir.path());
-		// Simulate a resumed session: append a message so the file exists, then setAdditionalDirectories.
-		session.appendMessage({ role: "user", content: "hello", timestamp: 1 });
+		// Simulate a resumed session: append an assistant message so the file exists, then setAdditionalDirectories.
+		session.appendMessage(makeAssistantMessage());
 		await session.flush();
 
 		await session.setAdditionalDirectories([path.join(tempDir.path(), "added")]);
@@ -164,11 +165,29 @@ describe("SessionManager workspace directories", () => {
 		expect(header.additionalDirectories).toEqual([path.join(tempDir.path(), "added")]);
 	});
 
+	it("keeps seeded roots in memory until the session is durable (no empty session file)", async () => {
+		using tempDir = TempDir.createSync("@pi-session-workspace-lazy-");
+		const session = SessionManager.create(tempDir.path(), tempDir.path());
+		await session.setAdditionalDirectories([path.join(tempDir.path(), "extra")]);
+		await session.addWorkspaceDirectory(path.join(tempDir.path(), "extra2"));
+		// Seeding roots must not materialize an empty resumable session file.
+		expect(fs.readdirSync(tempDir.path()).filter(f => f.endsWith(".jsonl"))).toEqual([]);
+
+		// Once the session produces durable output, the header carries the roots.
+		session.appendMessage(makeAssistantMessage());
+		await session.flush();
+		const reopened = await SessionManager.open(session.getSessionFile()!);
+		expect(reopened.getAdditionalDirectories()).toEqual([
+			path.join(tempDir.path(), "extra"),
+			path.join(tempDir.path(), "extra2"),
+		]);
+	});
+
 	it("forkFrom preserves additionalDirectories from the source session", async () => {
 		using tempDir = TempDir.createSync("@pi-session-workspace-fork-");
 		const source = SessionManager.create(tempDir.path(), tempDir.path());
 		await source.addWorkspaceDirectory(path.join(tempDir.path(), "extra"));
-		source.appendMessage({ role: "user", content: "hello", timestamp: 1 });
+		source.appendMessage(makeAssistantMessage());
 		await source.flush();
 
 		const forked = await SessionManager.forkFrom(source.getSessionFile()!, tempDir.path());