diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index d666c1d4..b1523882 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -259,7 +259,6 @@ export class DefaultPackageManager implements PackageManager {
 		this.cwd = options.cwd;
 		this.agentDir = options.agentDir;
 		this.settingsManager = options.settingsManager;
-		this.ensureGitIgnoreDirs();
 	}
 
 	setProgressCallback(callback: ProgressCallback | undefined): void {
@@ -623,6 +622,10 @@ export class DefaultPackageManager implements PackageManager {
 		if (existsSync(targetDir)) {
 			return;
 		}
+		const gitRoot = this.getGitInstallRoot(scope);
+		if (gitRoot) {
+			this.ensureGitIgnore(gitRoot);
+		}
 		mkdirSync(dirname(targetDir), { recursive: true });
 		const cloneUrl = source.repo.startsWith("http") ? source.repo : `https://${source.repo}`;
 		await this.runCommand("git", ["clone", cloneUrl, targetDir]);
@@ -666,13 +669,6 @@ export class DefaultPackageManager implements PackageManager {
 		}
 	}
 
-	private ensureGitIgnoreDirs(): void {
-		this.ensureGitIgnore(join(this.agentDir, "git"));
-		this.ensureGitIgnore(join(this.agentDir, "npm"));
-		this.ensureGitIgnore(join(this.cwd, CONFIG_DIR_NAME, "git"));
-		this.ensureGitIgnore(join(this.cwd, CONFIG_DIR_NAME, "npm"));
-	}
-
 	private ensureGitIgnore(dir: string): void {
 		if (!existsSync(dir)) {
 			mkdirSync(dir, { recursive: true });
@@ -722,6 +718,16 @@ export class DefaultPackageManager implements PackageManager {
 		return join(this.agentDir, "git", source.host, source.path);
 	}
 
+	private getGitInstallRoot(scope: SourceScope): string | undefined {
+		if (scope === "temporary") {
+			return undefined;
+		}
+		if (scope === "project") {
+			return join(this.cwd, CONFIG_DIR_NAME, "git");
+		}
+		return join(this.agentDir, "git");
+	}
+
 	private getTemporaryDir(prefix: string, suffix?: string): string {
 		const hash = createHash("sha256")
 			.update(`${prefix}-${suffix ?? ""}`)