Keep new worktrees clean when setup changes are uncommitted (#3311)

* fix(worktrees): preserve selected base config

New worktrees were overwriting the selected ref's paseo.json with source-checkout bytes, which could create an accidental revert in an otherwise fresh workspace. Keep committed base config authoritative and warn when locally saved setup changes still need to be committed.

* fix(worktrees): seed config exclusively

* fix(projects): refresh config status on focus

packages/app/e2e/browser/projects-settings.spec.ts

@@ -9,12 +9,14 @@ import {
   clickReloadProjectSettings,
   clickRetryProjectSettingsSave,
   clickSaveProjectSettings,
+  commitPaseoConfig,
   corruptPaseoConfig,
   editWorktreeSetup,
   expectEmptyScriptList,
   expectProjectHostContextHidden,
   expectNoEditableTarget,
   expectNoProjectSettingsError,
+  expectNoUncommittedSetupWarning,
   expectProjectEditFailed,
   expectProjectEditName,
   expectProjectEditSaved,
@@ -27,6 +29,7 @@ import {
   expectSaveButtonDisabled,
   expectScriptRowCount,
   expectWriteFailedCalloutActions,
+  expectUncommittedSetupWarning,
   fillProjectIconUrl,
   fillProjectName,
   installDaemonConnectionGate,
@@ -216,9 +219,16 @@ test.describe("Projects settings", () => {
   test("user edits worktree setup from the projects page", async ({ page, editableProject }) => {
     await openProjects(page);
     await openProjectSettings(page, editableProject.name);
+    await expectNoUncommittedSetupWarning(page);
     await editWorktreeSetup(page, updatedSetup);
     await clickSaveProjectSettings(page);
     await expectProjectConfigSaved(editableProject);
+    await expectUncommittedSetupWarning(page);
+
+    commitPaseoConfig(editableProject.path);
+    await returnToProjectsList(page);
+    await openProjectSettings(page, editableProject.name);
+    await expectNoUncommittedSetupWarning(page);
   });
 
   test("project navigation stays inside the selected host", async ({ page, editableProject }) => {
@@ -439,5 +449,7 @@ test.describe("Projects settings — error UX", () => {
 
     await expectScriptRowCount(page, 0);
     await expectEmptyScriptList(page);
+    await clickSaveProjectSettings(page);
+    await expectNoUncommittedSetupWarning(page);
   });
 });

packages/app/e2e/support/helpers/project-settings.ts

@@ -1,4 +1,5 @@
 import { chmod, readFile, writeFile } from "node:fs/promises";
+import { execFileSync } from "node:child_process";
 import path from "node:path";
 import { expect, type Page } from "@playwright/test";
 import type { WebSocketRoute } from "@playwright/test";
@@ -177,6 +178,19 @@ export async function expectSaveButtonDisabled(page: Page): Promise<void> {
   await expect(page.getByTestId("save-button")).toBeDisabled();
 }
 
+export async function expectUncommittedSetupWarning(page: Page): Promise<void> {
+  const warning = page.getByRole("alert").filter({ hasText: "Commit paseo.json changes" });
+  await expect(warning).toContainText("Commit paseo.json changes");
+  await expect(warning).toContainText(
+    "New worktrees use the setup script from the base branch you select.",
+  );
+}
+
+export async function expectNoUncommittedSetupWarning(page: Page): Promise<void> {
+  const warning = page.getByRole("alert").filter({ hasText: "Commit paseo.json changes" });
+  await expect(warning).toHaveCount(0);
+}
+
 // --- Form-state assertions ---
 
 export async function expectProjectSettingsFormVisible(page: Page): Promise<void> {
@@ -249,6 +263,11 @@ export async function restorePaseoConfig(
   await writeFile(path.join(repoPath, "paseo.json"), JSON.stringify(config, null, 2) + "\n");
 }
 
+export function commitPaseoConfig(repoPath: string): void {
+  execFileSync("git", ["add", "paseo.json"], { cwd: repoPath });
+  execFileSync("git", ["commit", "-m", "Update project config"], { cwd: repoPath });
+}
+
 // The daemon writes atomically via a temp file + rename, so blocking writes requires
 // removing write permission from the *directory*, not just the file.
 export async function blockPaseoConfigWrites(repoPath: string): Promise<void> {