[codex] Add local Cloud Upstream sync (#6548)

## Thinking Path

> - Paperclip is the control plane for AI-agent companies.
> - Operators need a path to move local company state toward Paperclip
Cloud without losing local-first control.
> - The Cloud Upstream flow needs API, persistence, CLI, and board UI
surfaces that agree on the same manifest/run model.
> - The existing branch had the feature work plus UX and error-handling
follow-ups.
> - This pull request packages the remaining Cloud Upstream sync work
into one standalone branch.
> - The benefit is an inspectable local-to-cloud sync workflow with
preview, conflicts, activation, and captured UX review states.

## What Changed

- Added Cloud Upstream shared types, server routes/services, and
persisted run schema/migration.
- Added Paperclip Cloud CLI sync helpers and local connection storage.
- Added the Cloud Upstream board UI, settings entry points, query keys,
and UX lab page.
- Added preview/activation checklist behavior, redirect handling,
manifest-only preview support, friendly errors, in-flight hints, and
entity count summaries.

## Verification

- `pnpm --filter @paperclipai/plugin-sdk build`
- `NODE_ENV=test pnpm exec vitest run cli/src/__tests__/cloud.test.ts
server/src/__tests__/instance-settings-routes.test.ts
server/src/__tests__/instance-settings-service.test.ts
ui/src/pages/CloudUpstream.test.tsx
ui/src/components/CompanySettingsSidebar.test.tsx`
- `NODE_ENV=test pnpm exec vitest run
server/src/__tests__/cloud-upstreams.test.ts`

Worktree setup note: the isolated worktree install skipped native sqlite
build scripts, so I copied the already-built local sqlite binding from
the main checkout before running
`server/src/__tests__/cloud-upstreams.test.ts`. The test then passed.

## Risks

- Medium: this adds a database migration and a broad feature path across
CLI/server/UI.
- Merge order: this is the only PR in this split with a DB migration;
merge it before any future Cloud Upstream migration follow-up.
- Mitigation: the PR is based directly on current `origin/master`, has
targeted route/service/UI tests, and keeps the feature behind existing
experimental Cloud Sync settings.

> 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 GPT-5 Codex via `codex_local`, tool-enabled coding session;
exact context window not exposed by this 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, screenshot artifacts are
intentionally omitted per reviewer request
- [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

server/src/services/companies.ts

@@ -265,7 +265,17 @@ export function companyService(db: Db) {
     remove: (id: string) =>
       db.transaction(async (tx) => {
         // Delete from child tables in dependency order
+        const companyRunIds = await tx
+          .select({ id: heartbeatRuns.id })
+          .from(heartbeatRuns)
+          .where(eq(heartbeatRuns.companyId, id));
+
         await tx.delete(heartbeatRunEvents).where(eq(heartbeatRunEvents.companyId, id));
+        if (companyRunIds.length > 0) {
+          await tx
+            .delete(heartbeatRunEvents)
+            .where(inArray(heartbeatRunEvents.runId, companyRunIds.map((run) => run.id)));
+        }
         await tx.delete(agentTaskSessions).where(eq(agentTaskSessions.companyId, id));
         await tx.delete(activityLog).where(eq(activityLog.companyId, id));
         await tx.delete(heartbeatRuns).where(eq(heartbeatRuns.companyId, id));

server/src/services/index.ts

@@ -59,6 +59,7 @@ export type {
 } from "./authorization.js";
 export { boardAuthService } from "./board-auth.js";
 export { instanceSettingsService } from "./instance-settings.js";
+export { cloudUpstreamService, reconcileCloudUpstreamRunsOnStartup } from "./cloud-upstreams.js";
 export { companyPortabilityService } from "./company-portability.js";
 export { environmentService } from "./environments.js";
 export { executionWorkspaceService } from "./execution-workspaces.js";

server/src/services/instance-settings.ts

@@ -15,9 +15,11 @@ import {
 import { eq } from "drizzle-orm";
 
 const DEFAULT_SINGLETON_KEY = "default";
+const instanceGeneralSettingsStorageSchema = instanceGeneralSettingsSchema.strip();
+const instanceExperimentalSettingsStorageSchema = instanceExperimentalSettingsSchema.strip();
 
 function normalizeGeneralSettings(raw: unknown): InstanceGeneralSettings {
-  const parsed = instanceGeneralSettingsSchema.safeParse(raw ?? {});
+  const parsed = instanceGeneralSettingsStorageSchema.safeParse(raw ?? {});
   if (parsed.success) {
     return {
       censorUsernameInLogs: parsed.data.censorUsernameInLogs ?? false,
@@ -35,12 +37,13 @@ function normalizeGeneralSettings(raw: unknown): InstanceGeneralSettings {
   };
 }
 
-function normalizeExperimentalSettings(raw: unknown): InstanceExperimentalSettings {
-  const parsed = instanceExperimentalSettingsSchema.safeParse(raw ?? {});
+export function normalizeExperimentalSettings(raw: unknown): InstanceExperimentalSettings {
+  const parsed = instanceExperimentalSettingsStorageSchema.safeParse(raw ?? {});
   if (parsed.success) {
     return {
       enableEnvironments: parsed.data.enableEnvironments ?? false,
       enableIsolatedWorkspaces: parsed.data.enableIsolatedWorkspaces ?? false,
+      enableCloudSync: parsed.data.enableCloudSync ?? false,
       autoRestartDevServerWhenIdle: parsed.data.autoRestartDevServerWhenIdle ?? false,
       enableIssueGraphLivenessAutoRecovery: parsed.data.enableIssueGraphLivenessAutoRecovery ?? false,
       issueGraphLivenessAutoRecoveryLookbackHours:
@@ -51,6 +54,7 @@ function normalizeExperimentalSettings(raw: unknown): InstanceExperimentalSettin
   return {
     enableEnvironments: false,
     enableIsolatedWorkspaces: false,
+    enableCloudSync: false,
     autoRestartDevServerWhenIdle: false,
     enableIssueGraphLivenessAutoRecovery: false,
     issueGraphLivenessAutoRecoveryLookbackHours: