[codex] Add plugin orchestration host APIs (#4114)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system is the extension path for optional capabilities
that should not require core product changes for every integration.
> - Plugins need scoped host APIs for issue orchestration, documents,
wakeups, summaries, activity attribution, and isolated database state.
> - Without those host APIs, richer plugins either cannot coordinate
Paperclip work safely or need privileged core-side special cases.
> - This pull request adds the plugin orchestration host surface, scoped
route dispatch, a database namespace layer, and a smoke plugin that
exercises the contract.
> - The benefit is a broader plugin API that remains company-scoped,
auditable, and covered by tests.

## What Changed

- Added plugin orchestration host APIs for issue creation, document
access, wakeups, summaries, plugin-origin activity, and scoped API route
dispatch.
- Added plugin database namespace tables, schema exports, migration
checks, and idempotent replay coverage under migration
`0059_plugin_database_namespaces`.
- Added shared plugin route/API types and validators used by server and
SDK boundaries.
- Expanded plugin SDK types, protocol helpers, worker RPC host behavior,
and testing utilities for orchestration flows.
- Added the `plugin-orchestration-smoke-example` package to exercise
scoped routes, restricted database namespaces, issue orchestration,
documents, wakeups, summaries, and UI status surfaces.
- Kept the new orchestration smoke fixture out of the root pnpm
workspace importer so this PR preserves the repository policy of not
committing `pnpm-lock.yaml`.
- Updated plugin docs and database docs for the new orchestration and
database namespace surfaces.
- Rebased the branch onto `public-gh/master`, resolved conflicts, and
removed `pnpm-lock.yaml` from the final PR diff.

## Verification

- `pnpm install --frozen-lockfile`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm exec vitest run packages/db/src/client.test.ts`
- `pnpm exec vitest run server/src/__tests__/plugin-database.test.ts
server/src/__tests__/plugin-orchestration-apis.test.ts
server/src/__tests__/plugin-routes-authz.test.ts
server/src/__tests__/plugin-scoped-api-routes.test.ts
server/src/__tests__/plugin-sdk-orchestration-contract.test.ts`
- From `packages/plugins/examples/plugin-orchestration-smoke-example`:
`pnpm exec vitest run --config ./vitest.config.ts`
- `pnpm --dir
packages/plugins/examples/plugin-orchestration-smoke-example run
typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- PR CI on latest head `293fc67c`: `policy`, `verify`, `e2e`, and
`security/snyk` all passed.

## Risks

- Medium risk: this expands plugin host authority, so route auth,
company scoping, and plugin-origin activity attribution need careful
review.
- Medium risk: database namespace migration behavior must remain
idempotent for environments that may have seen earlier branch versions.
- Medium risk: the orchestration smoke fixture is intentionally excluded
from the root workspace importer to avoid a `pnpm-lock.yaml` PR diff;
direct fixture verification remains listed above.
- Low operational risk from the PR setup itself: the branch is rebased
onto current `master`, the migration is ordered after upstream
`0057`/`0058`, and `pnpm-lock.yaml` is not in the final diff.

> 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`.

Roadmap checked: this work aligns with the completed Plugin system
milestone and extends the plugin surface rather than duplicating an
unrelated planned core feature.

## Model Used

- OpenAI Codex, GPT-5-based coding agent in a tool-enabled CLI
environment. Exact hosted model build and context-window size are not
exposed by the runtime; reasoning/tool use were enabled for repository
inspection, editing, testing, git operations, and PR creation.

## 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 (N/A: no core UI screen change; example plugin UI contract
is covered by tests)
- [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/services/heartbeat.ts

@@ -2,6 +2,7 @@ import fs from "node:fs/promises";
 import path from "node:path";
 import { execFile as execFileCallback } from "node:child_process";
 import { promisify } from "node:util";
+import { randomUUID } from "node:crypto";
 import { and, asc, desc, eq, getTableColumns, gt, inArray, isNull, or, sql } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
 import {
@@ -60,7 +61,7 @@ import {
   classifyRunLiveness,
   type RunLivenessClassificationInput,
 } from "./run-liveness.js";
-import { logActivity, type LogActivityInput } from "./activity-log.js";
+import { logActivity, publishPluginDomainEvent, type LogActivityInput } from "./activity-log.js";
 import {
   buildWorkspaceReadyComment,
   cleanupExecutionWorkspaceArtifacts,
@@ -2377,11 +2378,50 @@ export function heartbeatService(db: Db) {
           finishedAt: updated.finishedAt ? new Date(updated.finishedAt).toISOString() : null,
         },
       });
+      publishRunLifecyclePluginEvent(updated);
     }
 
     return updated;
   }
 
+  function publishRunLifecyclePluginEvent(run: typeof heartbeatRuns.$inferSelect) {
+    const eventType =
+      run.status === "running"
+        ? "agent.run.started"
+        : run.status === "succeeded"
+          ? "agent.run.finished"
+          : run.status === "failed" || run.status === "timed_out"
+            ? "agent.run.failed"
+            : run.status === "cancelled"
+              ? "agent.run.cancelled"
+              : null;
+    if (!eventType) return;
+    publishPluginDomainEvent({
+      eventId: randomUUID(),
+      eventType,
+      occurredAt: new Date().toISOString(),
+      actorId: run.agentId,
+      actorType: "agent",
+      entityId: run.id,
+      entityType: "heartbeat_run",
+      companyId: run.companyId,
+      payload: {
+        runId: run.id,
+        agentId: run.agentId,
+        status: run.status,
+        invocationSource: run.invocationSource,
+        triggerDetail: run.triggerDetail,
+        error: run.error ?? null,
+        errorCode: run.errorCode ?? null,
+        issueId: typeof run.contextSnapshot === "object" && run.contextSnapshot !== null
+          ? (run.contextSnapshot as Record<string, unknown>).issueId ?? null
+          : null,
+        startedAt: run.startedAt ? new Date(run.startedAt).toISOString() : null,
+        finishedAt: run.finishedAt ? new Date(run.finishedAt).toISOString() : null,
+      },
+    });
+  }
+
   async function setWakeupStatus(
     wakeupRequestId: string | null | undefined,
     status: string,
@@ -3054,6 +3094,7 @@ export function heartbeatService(db: Db) {
         finishedAt: claimed.finishedAt ? new Date(claimed.finishedAt).toISOString() : null,
       },
     });
+    publishRunLifecyclePluginEvent(claimed);
 
     await setWakeupStatus(claimed.wakeupRequestId, "claimed", { claimedAt });