[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/plugin-capability-validator.ts

@@ -51,6 +51,7 @@ const OPERATION_CAPABILITIES: Record<string, readonly PluginCapability[]> = {
   "project.workspaces.get": ["project.workspaces.read"],
   "issues.list": ["issues.read"],
   "issues.get": ["issues.read"],
+  "issues.relations.get": ["issue.relations.read"],
   "issue.comments.list": ["issue.comments.read"],
   "issue.comments.get": ["issue.comments.read"],
   "agents.list": ["agents.read"],
@@ -61,14 +62,26 @@ const OPERATION_CAPABILITIES: Record<string, readonly PluginCapability[]> = {
   "activity.get": ["activity.read"],
   "costs.list": ["costs.read"],
   "costs.get": ["costs.read"],
+  "issues.summaries.getOrchestration": ["issues.orchestration.read"],
+  "db.namespace": ["database.namespace.read"],
+  "db.query": ["database.namespace.read"],
 
   // Data write operations
   "issues.create": ["issues.create"],
   "issues.update": ["issues.update"],
+  "issues.relations.setBlockedBy": ["issue.relations.write"],
+  "issues.relations.addBlockers": ["issue.relations.write"],
+  "issues.relations.removeBlockers": ["issue.relations.write"],
+  "issues.assertCheckoutOwner": ["issues.checkout"],
+  "issues.getSubtree": ["issue.subtree.read"],
+  "issues.requestWakeup": ["issues.wakeup"],
+  "issues.requestWakeups": ["issues.wakeup"],
   "issue.comments.create": ["issue.comments.create"],
   "activity.log": ["activity.log.write"],
   "metrics.write": ["metrics.write"],
   "telemetry.track": ["telemetry.track"],
+  "db.migrate": ["database.namespace.migrate"],
+  "db.execute": ["database.namespace.write"],
 
   // Plugin state operations
   "plugin.state.get": ["plugin.state.read"],
@@ -141,6 +154,7 @@ const FEATURE_CAPABILITIES: Record<string, PluginCapability> = {
   tools: "agent.tools.register",
   jobs: "jobs.schedule",
   webhooks: "webhooks.receive",
+  database: "database.namespace.migrate",
 };
 
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