Fix packaged-app launch crash, quit teardown, and broaden GitHub repo picker

apps/desktop/src/lib/trpc/routers/workspaces/procedures/delete.ts

@@ -1,5 +1,7 @@
 import { existsSync } from "node:fs";
+import { join } from "node:path";
 import type { SelectWorktree } from "@superset/local-db";
+import { getAgentHome, getAgentWorktreePath } from "main/lib/agent-home";
 import { track } from "main/lib/analytics";
 import { workspaceInitManager } from "main/lib/workspace-init-manager";
 import { getWorkspaceRuntimeRegistry } from "main/lib/workspace-runtime";
@@ -22,7 +24,11 @@ import {
 	hasUnpushedCommits,
 	worktreeExists,
 } from "../utils/git";
-import { removeWorktreeFromDisk, runTeardown } from "../utils/teardown";
+import {
+	removeAgentHomeFromDisk,
+	removeWorktreeFromDisk,
+	runTeardown,
+} from "../utils/teardown";
 
 export const createDeleteProcedures = () => {
 	return router({
@@ -44,6 +50,7 @@ export const createDeleteProcedures = () => {
 						activeTerminalCount: 0,
 						hasChanges: false,
 						hasUnpushedCommits: false,
+						isAgent: false,
 					};
 				}
 
@@ -55,6 +62,7 @@ export const createDeleteProcedures = () => {
 						activeTerminalCount: 0,
 						hasChanges: false,
 						hasUnpushedCommits: false,
+						isAgent: false,
 					};
 				}
 
@@ -71,6 +79,10 @@ export const createDeleteProcedures = () => {
 						activeTerminalCount,
 						hasChanges: false,
 						hasUnpushedCommits: false,
+						isAgent:
+							!!workspace.worktreeId &&
+							getWorktree(workspace.worktreeId)?.path ===
+								getAgentWorktreePath(workspace.id),
 					};
 				}
 
@@ -83,6 +95,10 @@ export const createDeleteProcedures = () => {
 						activeTerminalCount,
 						hasChanges: false,
 						hasUnpushedCommits: false,
+						isAgent:
+							!!workspace.worktreeId &&
+							getWorktree(workspace.worktreeId)?.path ===
+								getAgentWorktreePath(workspace.id),
 					};
 				}
 
@@ -92,22 +108,27 @@ export const createDeleteProcedures = () => {
 				const project = getProject(workspace.projectId);
 
 				if (worktree && project) {
+					// Papyrus Agents own a standalone clone at <agent-home>/worktree;
+					// it is NOT a `git worktree` of the Category's mainRepoPath, so
+					// check the clone directly instead of `git worktree list`.
+					const isAgent = worktree.path === getAgentWorktreePath(workspace.id);
 					try {
-						const exists = await worktreeExists(
-							project.mainRepoPath,
-							worktree.path,
-						);
+						const exists = isAgent
+							? existsSync(join(worktree.path, ".git"))
+							: await worktreeExists(project.mainRepoPath, worktree.path);
 
 						if (!exists) {
 							return {
 								canDelete: true,
 								reason: null,
 								workspace,
-								warning:
-									"Worktree not found in git (may have been manually removed)",
+								warning: isAgent
+									? "Agent repo not found on disk"
+									: "Worktree not found in git (may have been manually removed)",
 								activeTerminalCount,
 								hasChanges: false,
 								hasUnpushedCommits: false,
+								isAgent,
 							};
 						}
 
@@ -124,6 +145,7 @@ export const createDeleteProcedures = () => {
 							activeTerminalCount,
 							hasChanges,
 							hasUnpushedCommits: unpushedCommits,
+							isAgent,
 						};
 					} catch (error) {
 						return {
@@ -133,6 +155,7 @@ export const createDeleteProcedures = () => {
 							activeTerminalCount,
 							hasChanges: false,
 							hasUnpushedCommits: false,
+							isAgent,
 						};
 					}
 				}
@@ -145,6 +168,7 @@ export const createDeleteProcedures = () => {
 					activeTerminalCount,
 					hasChanges: false,
 					hasUnpushedCommits: false,
+					isAgent: false,
 				};
 			}),
 
@@ -248,14 +272,22 @@ export const createDeleteProcedures = () => {
 					}
 				}
 
+				// Agents own a standalone clone under their home dir — remove the
+				// whole home (worktree + memory + .codex) rather than `git worktree
+				// remove` against the Category's mainRepoPath (not a repo).
+				const isAgentRepo =
+					!!worktree && worktree.path === getAgentWorktreePath(input.id);
+
 				if (worktree && project) {
 					await workspaceInitManager.acquireProjectLock(project.id);
 
 					try {
-						const removeResult = await removeWorktreeFromDisk({
-							mainRepoPath: project.mainRepoPath,
-							worktreePath: worktree.path,
-						});
+						const removeResult = isAgentRepo
+							? await removeAgentHomeFromDisk(getAgentHome(input.id))
+							: await removeWorktreeFromDisk({
+									mainRepoPath: project.mainRepoPath,
+									worktreePath: worktree.path,
+								});
 						if (!removeResult.success) {
 							clearWorkspaceDeletingStatus(input.id);
 							return removeResult;
@@ -264,7 +296,7 @@ export const createDeleteProcedures = () => {
 						workspaceInitManager.releaseProjectLock(project.id);
 					}
 
-					if (input.deleteLocalBranch && workspace.branch) {
+					if (!isAgentRepo && input.deleteLocalBranch && workspace.branch) {
 						try {
 							await deleteLocalBranch({
 								mainRepoPath: project.mainRepoPath,

apps/desktop/src/lib/trpc/routers/workspaces/utils/teardown.ts

@@ -1,4 +1,8 @@
 import { spawn } from "node:child_process";
+import { randomUUID } from "node:crypto";
+import { existsSync } from "node:fs";
+import { rename } from "node:fs/promises";
+import { dirname, join } from "node:path";
 import {
 	getCommandShellArgs,
 	getShellEnv,
@@ -129,6 +133,42 @@ export async function runTeardown({
 	}
 }
 
+/**
+ * Papyrus: delete an Agent's entire home dir (worktree + memory + .codex).
+ * Agents own a standalone clone, not a `git worktree` of a main repo, so
+ * there is no worktree metadata to prune — just remove the directory.
+ * Same rename-then-background-rm pattern as removeWorktree in git.ts.
+ */
+export async function removeAgentHomeFromDisk(
+	agentHome: string,
+): Promise<{ success: true } | { success: false; error: string }> {
+	try {
+		if (!existsSync(agentHome)) {
+			return { success: true };
+		}
+		const tempPath = join(
+			dirname(agentHome),
+			`.papyrus-delete-${randomUUID()}`,
+		);
+		await rename(agentHome, tempPath);
+		const child = spawn("/bin/rm", ["-rf", tempPath], {
+			detached: true,
+			stdio: "ignore",
+		});
+		child.on("error", (err: Error) => {
+			console.error(
+				`[removeAgentHome] Failed to spawn rm for ${tempPath}:`,
+				err.message,
+			);
+		});
+		return { success: true };
+	} catch (error) {
+		const msg = error instanceof Error ? error.message : String(error);
+		console.error("Failed to remove agent home:", msg);
+		return { success: false, error: `Failed to remove agent files: ${msg}` };
+	}
+}
+
 export async function removeWorktreeFromDisk({
 	mainRepoPath,
 	worktreePath,

apps/desktop/src/main/index.ts

@@ -1,3 +1,8 @@
+// MUST be the first import: registers local-db host hooks before any module
+// (e.g. server-core's agent-memory-backfill → ./local-db) opens the DB and
+// runs migrations at module scope. Relying on the ./lib/local-db shim is not
+// enough — server-core modules import local-db relatively, bypassing the shim.
+import "./lib/local-db/register-host-hooks";
 import path from "node:path";
 import { pathToFileURL } from "node:url";
 import { settings } from "@superset/local-db";
@@ -152,19 +157,24 @@ export function setSkipQuitConfirmation(): void {
 
 export function quitWithoutConfirmation(): void {
 	skipConfirmation = true;
-	app.exit(0);
+	// Route through app.quit() so the before-quit teardown runs;
+	// app.exit() would bypass it.
+	app.quit();
 }
 
 app.on("before-quit", async (event) => {
 	if (isQuitting) return;
 
+	// Always preventDefault: this handler is async, and without it Electron
+	// exits before the teardown below runs on the non-confirm path. The
+	// app.exit(0) at the end performs the real quit.
+	event.preventDefault();
+
 	const isDev = process.env.NODE_ENV === "development";
 	const shouldConfirm =
 		!skipConfirmation && !isDev && getConfirmOnQuitSetting();
 
 	if (shouldConfirm) {
-		event.preventDefault();
-
 		try {
 			const { response } = await dialog.showMessageBox({
 				type: "question",

apps/desktop/src/renderer/components/NewAgentModal/NewAgentModal.tsx

@@ -199,7 +199,7 @@ export function NewAgentModal() {
 			open={isOpen}
 			onOpenChange={(open) => !open && closeModal()}
 		>
-			<DialogContent className="sm:max-w-[440px]">
+			<DialogContent className="max-h-[90vh] overflow-y-auto sm:max-w-[440px]">
 				<DialogHeader>
 					<DialogTitle>New agent</DialogTitle>
 				</DialogHeader>

apps/desktop/src/renderer/screens/main/components/WorkspaceSidebar/WorkspaceListItem/components/DeleteWorkspaceDialog/DeleteWorkspaceDialog.tsx

@@ -123,6 +123,7 @@ export function DeleteWorkspaceDialog({
 	};
 
 	const canDelete = canDeleteData?.canDelete ?? true;
+	const isAgent = canDeleteData?.isAgent ?? false;
 	const reason = canDeleteData?.reason;
 	const hasChanges = canDeleteData?.hasChanges ?? false;
 	const hasUnpushedCommits = canDeleteData?.hasUnpushedCommits ?? false;
@@ -196,8 +197,9 @@ export function DeleteWorkspaceDialog({
 								<span className="text-destructive">{reason}</span>
 							) : (
 								<span className="block">
-									Deleting will permanently remove the worktree. You can hide
-									instead to keep files on disk.
+									{isAgent
+										? "Deleting will permanently remove the agent's repo and memory from disk. You can hide instead to keep files on disk."
+										: "Deleting will permanently remove the worktree. You can hide instead to keep files on disk."}
 								</span>
 							)}
 						</div>
@@ -216,7 +218,7 @@ export function DeleteWorkspaceDialog({
 					</div>
 				)}
 
-				{!isLoading && canDelete && (
+				{!isLoading && canDelete && !isAgent && (
 					<div className="px-4 pb-2">
 						<div className="flex items-center gap-2">
 							<Checkbox
@@ -267,7 +269,9 @@ export function DeleteWorkspaceDialog({
 							</Button>
 						</TooltipTrigger>
 						<TooltipContent side="top" className="text-xs max-w-[200px]">
-							Permanently delete agent and git worktree from disk.
+							{isAgent
+								? "Permanently delete the agent, its repo, and its memory from disk."
+								: "Permanently delete agent and git worktree from disk."}
 						</TooltipContent>
 					</Tooltip>
 				</AlertDialogFooter>

packages/server-core/src/github-repos.ts

@@ -19,6 +19,14 @@ const GHRepoListItemSchema = z.object({
 
 export type GitHubRepoListItem = z.infer<typeof GHRepoListItemSchema>;
 
+// REST /user/repos item shape (only the fields the picker needs).
+const GHApiRepoSchema = z.object({
+	full_name: z.string(),
+	html_url: z.string(),
+	description: z.string().nullable(),
+	updated_at: z.string(),
+});
+
 export interface ListGitHubReposResult {
 	repos: GitHubRepoListItem[];
 	authenticated: boolean;
@@ -27,12 +35,53 @@ export interface ListGitHubReposResult {
 const REPO_LIST_LIMIT = 200;
 
 /**
- * Lists the authenticated user's GitHub repos via `gh repo list`. Never
- * throws — `gh` missing, not authenticated, or any other failure (network,
- * malformed output) all degrade to `{ repos: [], authenticated: false }` so
- * callers can render a "run `gh auth login`" hint instead of erroring.
+ * Lists the authenticated user's GitHub repos — personal AND org/collaborator
+ * repos — via the REST `/user/repos` endpoint (`gh repo list` only returns
+ * repos the user owns, which hides organization repos; see the affiliation
+ * param). `--paginate --slurp` yields a JSON array of pages. Never throws —
+ * `gh` missing, not authenticated, or any other failure (network, malformed
+ * output) all degrade to `{ repos: [], authenticated: false }` so callers can
+ * render a "run `gh auth login`" hint instead of erroring.
  */
 export async function listGitHubRepos(): Promise<ListGitHubReposResult> {
+	try {
+		const { stdout } = await execWithShellEnv("gh", [
+			"api",
+			"--paginate",
+			"--slurp",
+			"user/repos?affiliation=owner,collaborator,organization_member&sort=updated&per_page=100",
+		]);
+
+		const raw: unknown = JSON.parse(stdout);
+		if (!Array.isArray(raw)) {
+			return { repos: [], authenticated: false };
+		}
+
+		const repos: GitHubRepoListItem[] = [];
+		for (const page of raw) {
+			if (!Array.isArray(page)) continue;
+			for (const item of page) {
+				const result = GHApiRepoSchema.safeParse(item);
+				if (result.success) {
+					repos.push({
+						nameWithOwner: result.data.full_name,
+						url: result.data.html_url,
+						description: result.data.description,
+						updatedAt: result.data.updated_at,
+					});
+				}
+			}
+		}
+
+		return { repos: repos.slice(0, REPO_LIST_LIMIT), authenticated: true };
+	} catch {
+		// `gh api --slurp` needs a reasonably recent gh; fall back to the
+		// owner-only listing rather than losing the picker entirely.
+		return listOwnedGitHubRepos();
+	}
+}
+
+async function listOwnedGitHubRepos(): Promise<ListGitHubReposResult> {
 	try {
 		const { stdout } = await execWithShellEnv("gh", [
 			"repo",

packages/ui/src/components/ui/dialog.tsx

@@ -61,7 +61,7 @@ function DialogContent({
 			<DialogPrimitive.Content
 				data-slot="dialog-content"
 				className={cn(
-					"bg-background data-[state=open]:animate-in data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:fade-in-0 data-[state=closed]:zoom-out-95 data-[state=open]:zoom-in-95 fixed top-[50%] left-[50%] z-50 grid w-full max-w-[calc(100%-2rem)] translate-x-[-50%] translate-y-[-50%] gap-4 rounded-lg border p-6 shadow-lg duration-200 sm:max-w-lg",
+					"bg-background data-[state=open]:animate-in data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:fade-in-0 data-[state=closed]:zoom-out-95 data-[state=open]:zoom-in-95 fixed top-[50%] left-[50%] z-50 grid grid-cols-[minmax(0,1fr)] w-full max-w-[calc(100%-2rem)] translate-x-[-50%] translate-y-[-50%] gap-4 rounded-lg border p-6 shadow-lg duration-200 sm:max-w-lg",
 					className,
 				)}
 				{...props}