[codex] Add backup endpoint and dev runtime hardening (#4087)

## Thinking Path

> - Paperclip is a local-first control plane for AI-agent companies.
> - Operators need predictable local dev behavior, recoverable instance
data, and scripts that do not churn the running app.
> - Several accumulated changes improve backup streaming, dev-server
health, static UI caching/logging, diagnostic-file ignores, and instance
isolation.
> - These are operational improvements that can land independently from
product UI work.
> - This pull request groups the dev-infra and backup changes from the
split branch into one standalone branch.
> - The benefit is safer local operation, easier manual backups, less
noisy dev output, and less cross-instance auth leakage.

## What Changed

- Added a manual instance database backup endpoint and route tests.
- Streamed backup/restore handling to avoid materializing large payloads
at once.
- Reduced dev static UI log/cache churn and ignored Node diagnostic
report captures.
- Added guarded dev auto-restart health polling coverage.
- Preserved worktree config during provisioning and scoped auth cookies
by instance.
- Added a Discord daily digest helper script and environment
documentation.
- Hardened adapter-route and startup feedback export tests around the
changed infrastructure.

## Verification

- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run packages/db/src/backup-lib.test.ts
server/src/__tests__/instance-database-backups-routes.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/adapter-routes.test.ts
server/src/__tests__/dev-runner-paths.test.ts
server/src/__tests__/health-dev-server-token.test.ts
server/src/__tests__/http-log-policy.test.ts
server/src/__tests__/vite-html-renderer.test.ts
server/src/__tests__/workspace-runtime.test.ts
server/src/__tests__/better-auth.test.ts`
- Split integration check: merged after the runtime/governance branch
and before UI branches with no merge conflicts.
- Confirmed this branch does not include `pnpm-lock.yaml`.

## Risks

- Medium risk: touches server startup, backup streaming, auth cookie
naming, dev health checks, and worktree provisioning.
- Backup endpoint behavior depends on existing board/admin access
controls and database backup helpers.
- No database migrations are included.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5.4 tool-enabled coding model, agentic
code-editing/runtime with local shell and GitHub CLI access; exact
context window and reasoning mode are not exposed by the Paperclip
harness.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

server/src/app.ts

@@ -27,6 +27,10 @@ import { sidebarBadgeRoutes } from "./routes/sidebar-badges.js";
 import { sidebarPreferenceRoutes } from "./routes/sidebar-preferences.js";
 import { inboxDismissalRoutes } from "./routes/inbox-dismissals.js";
 import { instanceSettingsRoutes } from "./routes/instance-settings.js";
+import {
+  instanceDatabaseBackupRoutes,
+  type InstanceDatabaseBackupService,
+} from "./routes/instance-database-backups.js";
 import { llmRoutes } from "./routes/llms.js";
 import { authRoutes } from "./routes/auth.js";
 import { assetRoutes } from "./routes/assets.js";
@@ -112,6 +116,7 @@ export async function createApp(
         now?: Date;
       }): Promise<unknown>;
     };
+    databaseBackupService?: InstanceDatabaseBackupService;
     deploymentMode: DeploymentMode;
     deploymentExposure: DeploymentExposure;
     allowedHostnames: string[];
@@ -194,6 +199,9 @@ export async function createApp(
   api.use(sidebarPreferenceRoutes(db));
   api.use(inboxDismissalRoutes(db));
   api.use(instanceSettingsRoutes(db));
+  if (opts.databaseBackupService) {
+    api.use(instanceDatabaseBackupRoutes(opts.databaseBackupService));
+  }
   const hostServicesDisposers = new Map<string, () => void>();
   const workerManager = createPluginWorkerManager();
   const pluginRegistry = pluginRegistryService(db);