Expand plugin host surface (#5205)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - The plugin system is the extension boundary for optional product
capabilities
> - Rich plugins need more than a worker entrypoint: they need scoped
database storage, local project folders, managed agents/routines, host
navigation, and reusable UI components
> - The LLM Wiki work exposed those missing host surfaces while keeping
plugin code outside the core control plane
> - This pull request expands the core plugin host, SDK, server APIs,
and UI bridge so plugins can declare and use those surfaces
> - The benefit is that future plugins can integrate with Paperclip
through documented, validated contracts instead of bespoke server or UI
imports

## What Changed

- Added plugin-managed database namespaces and migration tracking,
including Drizzle schema/migration files and SQL validation for
namespace isolation.
- Added server support for plugin local folders, managed agents, managed
routines, scoped plugin APIs, and plugin operation visibility.
- Expanded shared plugin manifest/types/validators and SDK
host/testing/UI exports for richer plugin surfaces.
- Added reusable UI pieces for file trees, managed routines, resizable
sidebars, route sidebars, and plugin bridge initialization.
- Updated plugin docs and example plugins to use the expanded host and
SDK surface.

## Verification

- `pnpm install --frozen-lockfile`
- `pnpm run preflight:workspace-links && pnpm exec vitest run
packages/shared/src/validators/plugin.test.ts
server/src/__tests__/plugin-database.test.ts
server/src/__tests__/plugin-local-folders.test.ts
server/src/__tests__/plugin-managed-agents.test.ts
server/src/__tests__/plugin-managed-routines.test.ts
server/src/__tests__/plugin-orchestration-apis.test.ts
ui/src/api/plugins.test.ts ui/src/components/FileTree.test.tsx
ui/src/components/ResizableSidebarPane.test.tsx
ui/src/pages/PluginPage.test.tsx ui/src/plugins/bridge.test.ts` passed:
11 files, 67 tests.
- Confirmed this PR changes 89 files and does not include
`pnpm-lock.yaml` or `.github/workflows/*`.

## Risks

- Medium: this expands plugin host contracts across db/shared/server/ui
and includes a new core migration (`0076_useful_elektra.sql`).
- The plugin database namespace validator is intentionally restrictive;
plugin authors may need follow-up affordances for SQL patterns that
remain blocked.
- Merge this before the LLM Wiki plugin PR so the plugin can resolve the
new SDK and host APIs.

> 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 coding agent, tool-enabled shell/git/GitHub
workflow. Context window size was not exposed by the 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/services/issues.ts

@@ -1,5 +1,5 @@
 import { Buffer } from "node:buffer";
-import { and, asc, desc, eq, gt, inArray, isNull, lt, ne, notInArray, or, sql } from "drizzle-orm";
+import { and, asc, desc, eq, gt, inArray, isNull, like, lt, ne, notInArray, or, sql } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
 import {
   activityLog,
@@ -127,9 +127,11 @@ export interface IssueFilters {
   descendantOf?: string;
   labelId?: string;
   originKind?: string;
+  originKindPrefix?: string;
   originId?: string;
   includeRoutineExecutions?: boolean;
   excludeRoutineExecutions?: boolean;
+  includePluginOperations?: boolean;
   includeBlockedBy?: boolean;
   q?: string;
   limit?: number;
@@ -563,6 +565,19 @@ function inboxVisibleForUserCondition(companyId: string, userId: string) {
   `;
 }
 
+function nonPluginOperationIssueCondition() {
+  return sql<boolean>`NOT (${issues.originKind} LIKE 'plugin:%:operation' OR ${issues.originKind} LIKE 'plugin:%:operation:%')`;
+}
+
+function shouldIncludePluginOperationIssues(filters: IssueFilters | undefined) {
+  return Boolean(
+    filters?.includePluginOperations ||
+    filters?.originKind ||
+    filters?.originId ||
+    filters?.projectId,
+  );
+}
+
 /** Named entities commonly emitted in saved issue bodies; unknown `&name;` sequences are left unchanged. */
 const WELL_KNOWN_NAMED_HTML_ENTITIES: Readonly<Record<string, string>> = {
   amp: "&",
@@ -2201,7 +2216,11 @@ export function issueService(db: Db) {
       }
       if (filters?.parentId) conditions.push(eq(issues.parentId, filters.parentId));
       if (filters?.originKind) conditions.push(eq(issues.originKind, filters.originKind));
+      if (filters?.originKindPrefix) conditions.push(like(issues.originKind, `${filters.originKindPrefix}%`));
       if (filters?.originId) conditions.push(eq(issues.originId, filters.originId));
+      if (!shouldIncludePluginOperationIssues(filters)) {
+        conditions.push(nonPluginOperationIssueCondition());
+      }
       if (filters?.labelId) {
         const labeledIssueIds = await db
           .select({ issueId: issueLabels.issueId })
@@ -2333,6 +2352,7 @@ export function issueService(db: Db) {
       const conditions = [
         eq(issues.companyId, companyId),
         isNull(issues.hiddenAt),
+        nonPluginOperationIssueCondition(),
         unreadForUserCondition(companyId, userId),
       ];
       if (status) {