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>

packages/plugins/sdk/src/protocol.ts

@@ -29,8 +29,14 @@ import type {
   IssueDocumentSummary,
   IssueThreadInteraction,
   CreateIssueThreadInteraction,
+  PluginManagedAgentResolution,
+  PluginManagedProjectResolution,
+  PluginManagedRoutineResolution,
+  Routine,
+  RoutineRun,
   Agent,
   Goal,
+  PluginLocalFolderDeclaration,
 } from "@paperclipai/shared";
 export type { PluginLauncherRenderContextSnapshot } from "@paperclipai/shared";
 
@@ -46,6 +52,8 @@ import type {
   PluginWorkspace,
   ToolRunContext,
   ToolResult,
+  PluginLocalFolderListing,
+  PluginLocalFolderStatus,
 } from "./types.js";
 import type {
   PluginHealthDiagnostics,
@@ -566,6 +574,44 @@ export interface WorkerToHostMethods {
   // Config
   "config.get": [params: Record<string, never>, result: Record<string, unknown>];
 
+  // Trusted local folders
+  "localFolders.declarations": [
+    params: Record<string, never>,
+    result: PluginLocalFolderDeclaration[],
+  ];
+  "localFolders.configure": [
+    params: {
+      companyId: string;
+      folderKey: string;
+      path: string;
+      access?: "read" | "readWrite";
+      requiredDirectories?: string[];
+      requiredFiles?: string[];
+    },
+    result: PluginLocalFolderStatus,
+  ];
+  "localFolders.status": [
+    params: { companyId: string; folderKey: string },
+    result: PluginLocalFolderStatus,
+  ];
+  "localFolders.list": [
+    params: { companyId: string; folderKey: string; relativePath?: string | null; recursive?: boolean; maxEntries?: number },
+    result: PluginLocalFolderListing,
+  ];
+  "localFolders.readText": [
+    params: { companyId: string; folderKey: string; relativePath: string },
+    result: string,
+  ];
+  "localFolders.writeTextAtomic": [
+    params: {
+      companyId: string;
+      folderKey: string;
+      relativePath: string;
+      contents: string;
+    },
+    result: PluginLocalFolderStatus,
+  ];
+
   // State
   "state.get": [
     params: { scopeKind: string; scopeId?: string; namespace?: string; stateKey: string },
@@ -724,6 +770,57 @@ export interface WorkerToHostMethods {
     params: { issueId: string; companyId: string },
     result: PluginWorkspace | null,
   ];
+  "projects.managed.get": [
+    params: { projectKey: string; companyId: string },
+    result: PluginManagedProjectResolution,
+  ];
+  "projects.managed.reconcile": [
+    params: { projectKey: string; companyId: string },
+    result: PluginManagedProjectResolution,
+  ];
+  "projects.managed.reset": [
+    params: { projectKey: string; companyId: string },
+    result: PluginManagedProjectResolution,
+  ];
+  "routines.managed.get": [
+    params: { routineKey: string; companyId: string },
+    result: PluginManagedRoutineResolution,
+  ];
+  "routines.managed.reconcile": [
+    params: {
+      routineKey: string;
+      companyId: string;
+      assigneeAgentId?: string | null;
+      projectId?: string | null;
+    },
+    result: PluginManagedRoutineResolution,
+  ];
+  "routines.managed.reset": [
+    params: {
+      routineKey: string;
+      companyId: string;
+      assigneeAgentId?: string | null;
+      projectId?: string | null;
+    },
+    result: PluginManagedRoutineResolution,
+  ];
+  "routines.managed.update": [
+    params: {
+      routineKey: string;
+      companyId: string;
+      status?: string;
+    },
+    result: Routine,
+  ];
+  "routines.managed.run": [
+    params: {
+      routineKey: string;
+      companyId: string;
+      assigneeAgentId?: string | null;
+      projectId?: string | null;
+    },
+    result: RoutineRun,
+  ];
 
   // Issues
   "issues.list": [
@@ -732,8 +829,10 @@ export interface WorkerToHostMethods {
       projectId?: string;
       assigneeAgentId?: string;
       originKind?: string;
+      originKindPrefix?: string;
       originId?: string;
       status?: string;
+      includePluginOperations?: boolean;
       limit?: number;
       offset?: number;
     },
@@ -758,6 +857,7 @@ export interface WorkerToHostMethods {
       assigneeUserId?: string | null;
       requestDepth?: number;
       billingCode?: string | null;
+      surfaceVisibility?: string | null;
       originKind?: string | null;
       originId?: string | null;
       originRunId?: string | null;
@@ -940,6 +1040,18 @@ export interface WorkerToHostMethods {
     params: { agentId: string; companyId: string; prompt: string; reason?: string },
     result: { runId: string },
   ];
+  "agents.managed.get": [
+    params: { agentKey: string; companyId: string },
+    result: PluginManagedAgentResolution,
+  ];
+  "agents.managed.reconcile": [
+    params: { agentKey: string; companyId: string },
+    result: PluginManagedAgentResolution,
+  ];
+  "agents.managed.reset": [
+    params: { agentKey: string; companyId: string },
+    result: PluginManagedAgentResolution,
+  ];
 
   // Agent Sessions
   "agents.sessions.create": [