Fix empty project list when a project folder is deleted from disk

change-logs/2026/06/11/fix-deleted-project-folder-empty-board.md

@@ -0,0 +1 @@
+Fixed the dashboard showing an empty project list when one project's folder was deleted from disk — config resolution for a missing folder rejected the whole getProjects call. Each project now resolves independently and a broken one falls back to its stored settings. Also added daily projects.json backups (~/.dev3.0/projects-YYYY-MM-DD.json.bak, kept 7 days), written on startup and before each save.

src/bun/__tests__/data-projects-backup.test.ts

@@ -0,0 +1,104 @@
+import { describe, it, expect, vi, beforeEach } from "vitest";
+import { mkdirSync, readFileSync, readdirSync, rmSync, writeFileSync, existsSync } from "node:fs";
+import type { Project } from "../../shared/types";
+
+const TEST_HOME = "/tmp/dev3-test-projects-backup";
+
+vi.mock("../logger", () => ({
+	createLogger: () => ({
+		debug: vi.fn(),
+		info: vi.fn(),
+		warn: vi.fn(),
+		error: vi.fn(),
+	}),
+}));
+
+vi.mock("../paths", () => ({
+	DEV3_HOME: "/tmp/dev3-test-projects-backup",
+}));
+
+vi.mock("../cow-clone", () => ({
+	detectClonePaths: vi.fn(() => Promise.resolve([])),
+}));
+
+vi.mock("../file-lock", () => ({
+	withFileLock: async <T>(_filePath: string, fn: () => Promise<T>): Promise<T> => fn(),
+}));
+
+beforeEach(() => {
+	rmSync(TEST_HOME, { recursive: true, force: true });
+	mkdirSync(TEST_HOME, { recursive: true });
+});
+
+import { addProject, backupProjectsDaily, updateProject } from "../data";
+
+const PROJECTS_FILE = `${TEST_HOME}/projects.json`;
+
+function todayBackupFile(): string {
+	return `${TEST_HOME}/projects-${new Date().toISOString().slice(0, 10)}.json.bak`;
+}
+
+function listBackups(): string[] {
+	return readdirSync(TEST_HOME)
+		.filter((f) => /^projects-\d{4}-\d{2}-\d{2}\.json\.bak$/.test(f))
+		.sort();
+}
+
+function seedProjects(projects: Partial<Project>[]): void {
+	writeFileSync(PROJECTS_FILE, JSON.stringify(projects, null, 2));
+}
+
+describe("daily projects.json backups", () => {
+	it("writes a daily .bak with the pre-save content on first save of the day", async () => {
+		seedProjects([{ id: "old", name: "Old", path: "/tmp/old" } as Project]);
+
+		await addProject("/tmp/new-repo", "New Repo");
+
+		const backup = todayBackupFile();
+		expect(existsSync(backup)).toBe(true);
+		const backedUp = JSON.parse(readFileSync(backup, "utf-8"));
+		expect(backedUp).toHaveLength(1);
+		expect(backedUp[0].id).toBe("old");
+	});
+
+	it("does not overwrite the same day's backup on subsequent saves", async () => {
+		seedProjects([{ id: "old", name: "Old", path: "/tmp/old" } as Project]);
+
+		const added = await addProject("/tmp/new-repo", "New Repo");
+		await updateProject(added.id, { devScript: "bun run dev" });
+
+		const backedUp = JSON.parse(readFileSync(todayBackupFile(), "utf-8"));
+		expect(backedUp).toHaveLength(1);
+		expect(backedUp[0].id).toBe("old");
+	});
+
+	it("skips backup when there is no projects.json yet", async () => {
+		await addProject("/tmp/first-repo", "First Repo");
+
+		expect(listBackups()).toHaveLength(0);
+	});
+
+	it("prunes backups older than 7 days, keeping the newest 7", async () => {
+		seedProjects([{ id: "old", name: "Old", path: "/tmp/old" } as Project]);
+		for (let i = 1; i <= 9; i++) {
+			writeFileSync(`${TEST_HOME}/projects-2026-05-0${i}.json.bak`, "[]");
+		}
+
+		await addProject("/tmp/new-repo", "New Repo");
+
+		const backups = listBackups();
+		expect(backups).toHaveLength(7);
+		expect(backups).not.toContain("projects-2026-05-01.json.bak");
+		expect(backups).not.toContain("projects-2026-05-02.json.bak");
+		expect(backups).not.toContain("projects-2026-05-03.json.bak");
+		expect(backups[backups.length - 1]).toBe(todayBackupFile().split("/").pop());
+	});
+
+	it("backupProjectsDaily can be called standalone (startup hook)", async () => {
+		seedProjects([{ id: "p", name: "P", path: "/tmp/p" } as Project]);
+
+		await backupProjectsDaily();
+
+		expect(existsSync(todayBackupFile())).toBe(true);
+	});
+});

src/bun/__tests__/repo-config.test.ts

@@ -397,6 +397,36 @@ describe("migrateProjectConfig", () => {
 
 		expect(existsSync(join(TEST_DIR, ".dev3", "config.json"))).toBe(false);
 	});
+
+	it("does not recreate a deleted project folder", async () => {
+		const missingPath = join(TEST_DIR, "deleted-project");
+		const project = makeProject({ path: missingPath, setupScript: "bun install" });
+
+		await migrateProjectConfig(project);
+
+		expect(existsSync(missingPath)).toBe(false);
+	});
+});
+
+describe("resolveProjectConfig — deleted project folder resilience", () => {
+	it("resolves with fallback compare ref when detection fails on an existing path", async () => {
+		detectDefaultCompareRef.mockRejectedValue(new Error("spawn failed"));
+
+		const project = makeProject({ defaultCompareRef: undefined });
+		const resolved = await resolveProjectConfig(project);
+
+		expect(resolved.defaultCompareRef).toBe("main");
+	});
+
+	it("skips compare-ref detection entirely when the project folder is missing", async () => {
+		detectDefaultCompareRef.mockRejectedValue(new Error("ENOENT: no such cwd"));
+
+		const project = makeProject({ path: join(TEST_DIR, "gone"), defaultCompareRef: undefined });
+		const resolved = await resolveProjectConfig(project);
+
+		expect(detectDefaultCompareRef).not.toHaveBeenCalled();
+		expect(resolved.defaultCompareRef).toBe("main");
+	});
 });
 
 describe("hasRepoConfig", () => {

src/bun/__tests__/rpc-handlers.test.ts

@@ -939,6 +939,13 @@ describe("end-to-end: task description → shell command escaping", () => {
 describe("handlers.getProjects", () => {
 	beforeEach(() => vi.clearAllMocks());
 
+	// Restore module-level mock defaults — overridden implementations would
+	// otherwise leak into later describes (clearAllMocks keeps implementations).
+	afterEach(() => {
+		vi.mocked(repoConfig.resolveProjectConfig).mockImplementation((async (project: any) => project) as any);
+		vi.mocked(repoConfig.migrateProjectConfig).mockReset();
+	});
+
 	it("returns projects from data layer", async () => {
 		const projects = [makeProject(), makeProject({ id: "proj-2", name: "Second" })];
 		vi.mocked(data.loadProjects).mockResolvedValue(projects);
@@ -953,6 +960,28 @@ describe("handlers.getProjects", () => {
 		const result = await handlers.getProjects();
 		expect(result).toEqual([]);
 	});
+
+	it("still returns every project when config resolution fails for one (deleted folder)", async () => {
+		const ok = makeProject();
+		const broken = makeProject({ id: "proj-broken", path: "/tmp/deleted-from-disk" });
+		vi.mocked(data.loadProjects).mockResolvedValue([ok, broken]);
+		vi.mocked(repoConfig.resolveProjectConfig).mockImplementation(async (project: any) => {
+			if (project.id === "proj-broken") throw new Error("ENOENT: no such file or directory, posix_spawn");
+			return project;
+		});
+
+		const result = await handlers.getProjects();
+		expect(result.map((p) => p.id)).toEqual([ok.id, "proj-broken"]);
+	});
+
+	it("does not let a failing config migration drop the project list", async () => {
+		const project = makeProject();
+		vi.mocked(data.loadProjects).mockResolvedValue([project]);
+		vi.mocked(repoConfig.migrateProjectConfig).mockRejectedValue(new Error("disk gone"));
+
+		const result = await handlers.getProjects();
+		expect(result.map((p) => p.id)).toEqual([project.id]);
+	});
 });
 
 describe("handlers.reorderProjects", () => {

src/bun/data.ts

@@ -10,6 +10,8 @@ import { projectSlug } from "./git";
 const log = createLogger("data");
 
 const PROJECTS_FILE = `${DEV3_HOME}/projects.json`;
+const PROJECTS_BACKUP_RETENTION_DAYS = 7;
+const PROJECTS_BACKUP_FILE_PATTERN = /^projects-\d{4}-\d{2}-\d{2}\.json\.bak$/;
 const TASK_BACKUPS_DIR = "tasks-backups";
 const TASK_BACKUP_RETENTION_HOURS = 72;
 const TASK_BACKUP_FILE_PATTERN = /^\d{4}-\d{2}-\d{2}T\d{2}Z\.json$/;
@@ -177,11 +179,46 @@ async function rawLoadAllProjects(options?: { strict?: boolean; persistMigration
 async function rawSaveProjects(projects: Project[]): Promise<void> {
 	log.debug("Saving projects", { count: projects.length, file: PROJECTS_FILE });
 	await ensureDir(PROJECTS_FILE);
+	await backupProjectsDaily().catch((err) => {
+		log.warn("Failed to write daily projects backup (non-fatal)", { err });
+	});
 	await writeFile(PROJECTS_FILE, JSON.stringify(projects, null, 2));
 	projectsCache.delete(PROJECTS_FILE);
 	log.info(`Saved ${projects.length} project(s)`);
 }
 
+/**
+ * Snapshot projects.json to projects-YYYY-MM-DD.json.bak (once per day) and
+ * prune snapshots beyond the retention window. Called before every save and
+ * once at app startup. Writes new sibling files only — never moves or renames
+ * anything under ~/.dev3.0/ (see on-disk layout invariants in AGENTS.md).
+ */
+export async function backupProjectsDaily(now: Date = new Date()): Promise<void> {
+	let currentContent: string;
+	try {
+		currentContent = await readFile(PROJECTS_FILE, "utf8");
+	} catch (err: any) {
+		if (err.code === "ENOENT") return;
+		throw err;
+	}
+
+	const backupFile = `${DEV3_HOME}/projects-${now.toISOString().slice(0, 10)}.json.bak`;
+	try {
+		await readFile(backupFile, "utf8");
+	} catch (err: any) {
+		if (err.code !== "ENOENT") throw err;
+		await writeFile(backupFile, currentContent);
+		log.info("Wrote daily projects backup", { file: backupFile });
+	}
+
+	const backupFiles = (await readdir(DEV3_HOME))
+		.filter((entry) => PROJECTS_BACKUP_FILE_PATTERN.test(entry))
+		.sort();
+	for (const staleFile of backupFiles.slice(0, Math.max(0, backupFiles.length - PROJECTS_BACKUP_RETENTION_DAYS))) {
+		await unlink(`${DEV3_HOME}/${staleFile}`);
+	}
+}
+
 // ---- Projects (public API — all mutators use file lock) ----
 
 /** Load active (non-deleted) projects. */

src/bun/index.ts

@@ -216,6 +216,16 @@ if (shellEnv.sshAuthSock) {
 const cliSocketPath = startSocketServer();
 log.info("CLI socket server ready", { path: cliSocketPath });
 
+// Daily projects.json safety snapshot (projects-YYYY-MM-DD.json.bak, 7 days kept).
+// Saves also trigger it, but projects.json can go untouched for weeks — the
+// startup hook guarantees at least one fresh backup per day the app is used.
+{
+	const { backupProjectsDaily } = await import("./data");
+	backupProjectsDaily().catch((err) => {
+		log.warn("Startup projects backup failed (non-fatal)", { err });
+	});
+}
+
 // Side-effect: starts the PTY WebSocket server (dynamic import so PATH is patched first)
 const { setOnPtyDied, setOnBell, setOnIdle, setOnPaneExited, setOnOsc52Copy, getActiveSessionIds, getPtyPort } = await import("./pty-server");
 const { startPortScanPoller, stopPortScanPoller } = await import("./port-scanner");

src/bun/repo-config.ts

@@ -212,8 +212,22 @@ export async function resolveProjectConfig(project: Project, configPath?: string
 			? resolved.defaultBaseBranch
 			: `origin/${resolved.defaultBaseBranch}`;
 	} else if (resolved.defaultCompareRef === undefined) {
-		// Only auto-detect if no explicit value was set at any level (including project)
-		resolved.defaultCompareRef = await git.detectDefaultCompareRef(basePath, resolved.defaultBaseBranch);
+		// Only auto-detect if no explicit value was set at any level (including project).
+		// A deleted project folder (or any git/spawn failure) must not reject — one broken
+		// project would otherwise blow up the whole project list (Promise.all in getProjects).
+		if (!existsSync(basePath)) {
+			resolved.defaultCompareRef = resolved.defaultBaseBranch;
+		} else {
+			try {
+				resolved.defaultCompareRef = await git.detectDefaultCompareRef(basePath, resolved.defaultBaseBranch);
+			} catch (err) {
+				log.warn("Failed to detect default compare ref, falling back to base branch", {
+					path: basePath,
+					error: String(err),
+				});
+				resolved.defaultCompareRef = resolved.defaultBaseBranch;
+			}
+		}
 	}
 
 	return resolved;
@@ -230,6 +244,9 @@ export async function migrateProjectConfig(project: Project, configPath?: string
 	const repoPath = `${basePath}/${CONFIG_FILE}`;
 	const localPath = `${basePath}/${LOCAL_CONFIG_FILE}`;
 
+	// A deleted project folder must not be resurrected by mkdirSync in saveRepoConfig
+	if (!existsSync(basePath)) return;
+
 	// Skip if any .dev3/ config already exists
 	if (existsSync(repoPath) || existsSync(localPath)) return;
 

src/bun/rpc-handlers/app-handlers.ts

@@ -84,8 +84,21 @@ async function setWindowForeground(params: { focused: boolean }): Promise<void>
 async function getProjects(): Promise<Project[]> {
 	log.info("→ getProjects");
 	const rawProjects = await data.loadProjects();
-	await Promise.all(rawProjects.map((project) => repoConfig.migrateProjectConfig(project)));
-	const projects = await Promise.all(rawProjects.map((project) => repoConfig.resolveProjectConfig(project)));
+	// Per-project isolation: one broken project (e.g. its folder was deleted from
+	// disk) must never reject the whole list — that left users with an empty board.
+	const projects = await Promise.all(rawProjects.map(async (project) => {
+		try {
+			await repoConfig.migrateProjectConfig(project);
+			return await repoConfig.resolveProjectConfig(project);
+		} catch (err) {
+			log.warn("Failed to resolve project config, returning project as-is", {
+				id: project.id,
+				path: project.path,
+				error: String(err),
+			});
+			return project;
+		}
+	}));
 	log.info(`← getProjects: ${projects.length} project(s)`);
 	return projects;
 }

src/mainview/i18n/translations/en/tips.ts

@@ -212,6 +212,8 @@ const tips = {
 	"tip.statusColorRails.body": "Each task in the Active Tasks list has a colored left rail matching its status — scan who's working vs. waiting at a glance.",
 	"tip.skillAutocomplete.title": "Autocomplete agent skills with /",
 	"tip.skillAutocomplete.body": "Type / in a new task's description to pick an installed agent skill from the suggestion list.",
+	"tip.projectsDailyBackup.title": "Project list is backed up daily",
+	"tip.projectsDailyBackup.body": "Lost your projects? Restore from ~/.dev3.0/projects-YYYY-MM-DD.json.bak — snapshots are kept for 7 days.",
 } as const;
 
 export default tips;

src/mainview/i18n/translations/es/tips.ts

@@ -212,6 +212,8 @@ const tips = {
 	"tip.statusColorRails.body": "Cada tarea de la lista Tareas activas tiene una barra de color a la izquierda según su estado: distingue de un vistazo quién trabaja y quién espera.",
 	"tip.skillAutocomplete.title": "Autocompleta skills con /",
 	"tip.skillAutocomplete.body": "Escribe / en la descripción de una nueva tarea para elegir un skill de agente instalado de la lista de sugerencias.",
+	"tip.projectsDailyBackup.title": "Copia diaria de tus proyectos",
+	"tip.projectsDailyBackup.body": "¿Perdiste tus proyectos? Restáuralos desde ~/.dev3.0/projects-YYYY-MM-DD.json.bak — las copias se guardan 7 días.",
 };
 
 export default tips;

src/mainview/i18n/translations/ru/tips.ts

@@ -212,6 +212,8 @@ const tips = {
 	"tip.statusColorRails.body": "У каждой задачи в списке Active Tasks слева цветная полоса по её статусу — сразу видно, кто работает, а кто ждёт.",
 	"tip.skillAutocomplete.title": "Автодополнение скиллов через /",
 	"tip.skillAutocomplete.body": "Введите / в описании новой задачи, чтобы выбрать установленный скилл агента из списка подсказок.",
+	"tip.projectsDailyBackup.title": "Список проектов бэкапится ежедневно",
+	"tip.projectsDailyBackup.body": "Пропали проекты? Восстановите из ~/.dev3.0/projects-YYYY-MM-DD.json.bak — снимки хранятся 7 дней.",
 };
 
 export default tips;

src/mainview/tips.ts

@@ -675,6 +675,13 @@ const ALL_TIPS: Tip[] = [
 		bodyKey: "tip.skillAutocomplete.body",
 		icon: "\u{F0349}", // nf-md-magic_staff
 	},
+	// Batch 45: daily projects.json backups
+	{
+		id: "projects-daily-backup",
+		titleKey: "tip.projectsDailyBackup.title",
+		bodyKey: "tip.projectsDailyBackup.body",
+		icon: "\u{F006F}", // nf-md-backup_restore
+	},
 ];
 
 const COOLDOWN_MS = 3 * 24 * 60 * 60 * 1000; // 3 days