[codex] Runtime control-plane fixes (#6380)

## Thinking Path

> - Paperclip orchestrates AI agents through a server-side control plane
> - That control plane depends on reliable issue state transitions,
plugin lifecycle behavior, import limits, and startup/shutdown handling
> - Several small runtime fixes had accumulated on the working branch
and were mixed with larger feature work
> - Keeping them separate makes the correctness fixes reviewable and
mergeable without waiting for cloud-sync UI work
> - This pull request groups the server/runtime control-plane fixes into
one standalone branch
> - The benefit is a tighter, safer runtime baseline for retries,
imports, plugin migrations, feedback flushing, and trusted cloud import
handling

## What Changed

- Fixed updated issue list pagination sorting and scheduled retry
comment handling.
- Re-applied pending plugin migrations during hot reload and fixed
plugin-schema worktree seed restore.
- Hardened public tenant DB startup, portable import body limits,
trusted cloud import errors, and trusted cloud tenant import mutation
access.
- Expired stale request confirmations after user comments.
- Added feedback export shutdown hardening so database-unavailable flush
loops stop cleanly.
- Guarded plugin worker `error` event emission when no listener is
registered.

## Verification

- `pnpm install --frozen-lockfile --ignore-scripts`
- `pnpm --filter @paperclipai/plugin-sdk build`
- `npm run install --prefix
node_modules/.pnpm/sqlite3@5.1.7/node_modules/sqlite3`
- `pnpm exec vitest run server/src/__tests__/issues-service.test.ts
server/src/__tests__/plugin-lifecycle-restart.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/body-limits.test.ts
server/src/__tests__/feedback-flush-controller.test.ts
server/src/__tests__/error-handler.test.ts
server/src/__tests__/board-mutation-guard.test.ts
packages/db/src/backup-lib.test.ts` initially exposed local setup issues
and two 5s test timeouts.
- Rerun after local prereq build: `pnpm exec vitest run --testTimeout
15000 server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/feedback-flush-controller.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts` passed.
- Some embedded Postgres-backed tests skipped on this host because local
Postgres init was unavailable.

## Risks

- Runtime-touching branch: startup/shutdown and issue interaction
behavior should be reviewed carefully.
- The feedback export change disables repeated flush attempts only for
database connection-refused failures; other upload failures still log
normally.
- The plugin worker error guard avoids process crashes from unhandled
EventEmitter errors but may hide errors from code paths that expected an
emitted listener.

> 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-based coding agent with local shell/git/tool use.
Exact hosted model ID and context-window size are not exposed by the
local Paperclip adapter runtime.

## 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

@@ -59,6 +59,8 @@ import { pluginRegistryService } from "./services/plugin-registry.js";
 import { createHostClientHandlers } from "@paperclipai/plugin-sdk";
 import type { BetterAuthSessionResult } from "./auth/better-auth.js";
 import { createCachedViteHtmlRenderer } from "./vite-html-renderer.js";
+import { DEFAULT_JSON_BODY_LIMIT, PORTABLE_JSON_BODY_LIMIT } from "./http/body-limits.js";
+import { COMPANY_IMPORT_API_PATH } from "./routes/company-import-paths.js";
 
 type UiMode = "none" | "static" | "vite-dev";
 const FEEDBACK_EXPORT_FLUSH_INTERVAL_MS = 5_000;
@@ -81,6 +83,12 @@ const VITE_DEV_STATIC_PATHS = new Set([
   "/sw.js",
 ]);
 
+export function isDatabaseConnectionUnavailableError(err: unknown): boolean {
+  const error = err as { code?: unknown; message?: unknown; cause?: unknown };
+  if (error?.code === "ECONNREFUSED") return true;
+  return Boolean(error?.cause && isDatabaseConnectionUnavailableError(error.cause));
+}
+
 export function resolveViteHmrPort(serverPort: number): number {
   if (serverPort <= 55_535) {
     return serverPort + 10_000;
@@ -136,13 +144,17 @@ export async function createApp(
   },
 ) {
   const app = express();
+  const captureRawBody = (req: express.Request, _res: express.Response, buf: Buffer) => {
+    (req as unknown as { rawBody: Buffer }).rawBody = buf;
+  };
 
+  app.use(COMPANY_IMPORT_API_PATH, express.json({
+    limit: PORTABLE_JSON_BODY_LIMIT,
+    verify: captureRawBody,
+  }));
   app.use(express.json({
-    // Company import/export payloads can inline full portable packages.
-    limit: "10mb",
-    verify: (req, _res, buf) => {
-      (req as unknown as { rawBody: Buffer }).rawBody = buf;
-    },
+    limit: DEFAULT_JSON_BODY_LIMIT,
+    verify: captureRawBody,
   }));
   app.use(httpLogger);
   const privateHostnameGateEnabled = shouldEnablePrivateHostnameGuard({
@@ -404,18 +416,37 @@ export async function createApp(
 
   jobCoordinator.start();
   scheduler.start();
-  const feedbackExportTimer = opts.feedbackExportService
+  let feedbackExportShuttingDown = false;
+  let feedbackExportTimer: ReturnType<typeof setInterval> | null = null;
+  const disableFeedbackExportFlushes = () => {
+    feedbackExportShuttingDown = true;
+    if (feedbackExportTimer) {
+      clearInterval(feedbackExportTimer);
+      feedbackExportTimer = null;
+    }
+  };
+  const flushPendingFeedbackExports = async () => {
+    if (feedbackExportShuttingDown) return;
+    try {
+      await opts.feedbackExportService?.flushPendingFeedbackTraces();
+    } catch (err) {
+      if (isDatabaseConnectionUnavailableError(err)) {
+        disableFeedbackExportFlushes();
+        logger.warn({ err }, "Disabling pending feedback export flushes because the database is unavailable");
+        return;
+      }
+      logger.error({ err }, "Failed to flush pending feedback exports");
+    }
+  };
+
+  feedbackExportTimer = opts.feedbackExportService
     ? setInterval(() => {
-      void opts.feedbackExportService?.flushPendingFeedbackTraces().catch((err) => {
-        logger.error({ err }, "Failed to flush pending feedback exports");
-      });
+      void flushPendingFeedbackExports();
     }, FEEDBACK_EXPORT_FLUSH_INTERVAL_MS)
     : null;
   feedbackExportTimer?.unref?.();
   if (opts.feedbackExportService) {
-    void opts.feedbackExportService.flushPendingFeedbackTraces().catch((err) => {
-      logger.error({ err }, "Failed to flush pending feedback exports");
-    });
+    void flushPendingFeedbackExports();
   }
   void toolDispatcher.initialize().catch((err) => {
     logger.error({ err }, "Failed to initialize plugin tool dispatcher");
@@ -434,13 +465,19 @@ export async function createApp(
   }).catch((err) => {
     logger.error({ err }, "Failed to load ready plugins on startup");
   });
-  process.once("exit", () => {
-    if (feedbackExportTimer) clearInterval(feedbackExportTimer);
+  let appServicesShutdown = false;
+  const shutdownAppServices = () => {
+    if (appServicesShutdown) return;
+    appServicesShutdown = true;
+    disableFeedbackExportFlushes();
     devWatcher?.close();
     viteHtmlRenderer?.dispose();
     hostServiceCleanup.disposeAll();
     hostServiceCleanup.teardown();
-  });
+  };
+  app.locals.paperclipShutdown = shutdownAppServices;
+
+  process.once("exit", shutdownAppServices);
   process.once("beforeExit", () => {
     void flushPluginLogBuffer();
   });