[codex] Add LLM Wiki plugin package to master (#5716)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system is the extension surface for optional product
capabilities without baking every workflow into core.
> - The LLM Wiki plugin package was reviewed in stacked PR #5592, which
targeted `pap-9173-llm-wiki-rest`.
> - The stack base PR #5597 merged to `master` before #5592 was merged
into that branch, so the plugin package never reached `master`.
> - A direct PR from `pap-9173-llm-wiki-rest` back to `master` would be
noisy because that branch has diverged from current `master`.
> - This pull request reapplies the reviewed
`packages/plugins/plugin-llm-wiki/` package onto current `master` and
updates Docker deps-stage manifest coverage.
> - The branch intentionally no longer changes `pnpm-workspace.yaml`
after maintainer feedback; because the new package is now a root
workspace importer, the remaining integration question is how
maintainers want the root lockfile handled under the current PR policy.

## What Changed

- Added the LLM Wiki plugin package under
`packages/plugins/plugin-llm-wiki/` from the merged PR #5592 head.
- Preserved the post-review cleanup from #5592: generated
design/screenshot artifacts are not committed, and `src/ui/index.tsx` /
`src/wiki.ts` are small public entrypoints.
- Added the new plugin package manifest to the Docker deps stage so
policy can validate package manifest coverage.
- Removed the earlier `pnpm-workspace.yaml` exclusion per maintainer
request, so the plugin is included by the existing `packages/plugins/*`
workspace glob.

## Verification

Current head:
- PGlite migration harness: ran migrations 001-003, verified old
non-space distillation unique constraints were removed, inserted
duplicate cursor and work-item keys in a second space, then reran
migration 003 successfully
- `node ./scripts/check-docker-deps-stage.mjs`
- `git diff --check`

Known current-head install result after removing the workspace
exclusion:
- `pnpm install --frozen-lockfile` fails because `pnpm-lock.yaml` has no
importer for `packages/plugins/plugin-llm-wiki/package.json`.

Previously verified on the same plugin source before the
workspace-exclusion removal:
- `pnpm --filter @paperclipai/plugin-sdk build`
- `cd packages/plugins/plugin-llm-wiki && pnpm install --lockfile=false
&& pnpm test`

## Risks

- The branch now includes `packages/plugins/plugin-llm-wiki` in the root
workspace but does not update `pnpm-lock.yaml`. Root frozen install will
fail until maintainers choose a lockfile path that fits repo policy.
- Committing `pnpm-lock.yaml` directly on this PR conflicts with the
current PR policy check, while excluding the package from
`pnpm-workspace.yaml` was rejected in maintainer feedback.
- The package includes UI code already reviewed in #5592; generated
screenshot/design artifacts were intentionally removed per maintainer
request, so visual review should regenerate screenshots locally if
needed.
- The package depends on plugin host support from #5597, which is
already merged to `master`.

> 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 CLI, tool use and local code execution
enabled; context window not exposed.

## 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 the targeted checks listed above
- [x] I have added or updated tests where applicable
- [ ] 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

Stack context: #5592 was merged into `pap-9173-llm-wiki-rest` after
#5597 had already merged that branch to `master`, so this follow-up PR
is needed to carry the plugin package itself into `master`.

Co-authored-by: Paperclip <noreply@paperclip.ing>

packages/plugins/plugin-llm-wiki/tests/screenshots/capture.mjs

@@ -0,0 +1,167 @@
+#!/usr/bin/env node
+import { mkdirSync, copyFileSync, existsSync, readFileSync } from "node:fs";
+import { dirname, resolve, extname } from "node:path";
+import { fileURLToPath, pathToFileURL } from "node:url";
+import http from "node:http";
+import esbuild from "esbuild";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const pkgRoot = resolve(__dirname, "..", "..");
+const outDir = resolve(pkgRoot, "dist", "screenshots");
+const screensDir = resolve(pkgRoot, "screenshots");
+
+mkdirSync(outDir, { recursive: true });
+mkdirSync(screensDir, { recursive: true });
+
+const entry = resolve(__dirname, "entry.tsx");
+
+const repoRoot = resolve(pkgRoot, "..", "..", "..");
+const reactPath = resolve(repoRoot, "node_modules/.pnpm/react@19.2.4/node_modules/react");
+const reactDomPath = resolve(repoRoot, "node_modules/.pnpm/react-dom@19.2.4_react@19.2.4/node_modules/react-dom");
+
+console.log("Bundling screenshot harness…");
+await esbuild.build({
+  entryPoints: [entry],
+  bundle: true,
+  format: "esm",
+  platform: "browser",
+  target: "es2022",
+  outfile: resolve(outDir, "bundle.js"),
+  jsx: "automatic",
+  loader: { ".tsx": "tsx", ".ts": "ts" },
+  define: { "process.env.NODE_ENV": '"production"' },
+  logLevel: "warning",
+  alias: {
+    "react": reactPath,
+    "react-dom": reactDomPath,
+    "react-dom/client": resolve(reactDomPath, "client.js"),
+    "react/jsx-runtime": resolve(reactPath, "jsx-runtime.js"),
+  },
+});
+
+copyFileSync(resolve(__dirname, "index.html"), resolve(outDir, "index.html"));
+
+const desktopViewport = { width: 1440, height: 920 };
+const mobileViewport = { width: 390, height: 844 };
+
+const desktopTargets = [
+  { slug: "01-wiki-browse", view: "wiki-sidebar", section: null },
+  { slug: "02-wiki-ingest", view: "wiki-sidebar", section: "ingest" },
+  { slug: "03-wiki-query", view: "wiki-sidebar", section: "query" },
+  { slug: "04-wiki-lint", view: "wiki-sidebar", section: "lint" },
+  { slug: "05-wiki-history", view: "wiki-sidebar", section: "history" },
+  { slug: "06-wiki-settings", view: "wiki-sidebar", section: "settings" },
+  { slug: "07-host-settings", view: "settings" },
+  { slug: "09-sidebar-link", view: "sidebar" },
+  { slug: "11-wiki-distillation-settings", view: "wiki-sidebar", section: "settings/distillation" },
+  { slug: "12-wiki-distillation-unconfigured", view: "wiki-sidebar", section: "settings/distillation", search: "unconfigured=1" },
+  { slug: "20-spaces-sidebar", view: "wiki-sidebar", section: null },
+  { slug: "21-spaces-ingest", view: "wiki-sidebar", section: "ingest" },
+  { slug: "21a-spaces-ingest-with-disclaimer", view: "wiki-sidebar", section: "ingest" },
+  { slug: "22-spaces-edit", view: "wiki-sidebar", section: "settings/spaces/team-research", scrollToText: "Paperclip ingestion" },
+  { slug: "22a-spaces-edit-default", view: "wiki-sidebar", section: "settings/spaces/default", scrollToText: "Paperclip ingestion" },
+  { slug: "23-spaces-non-default-route", view: "wiki-sidebar", section: "spaces/team-research" },
+  { slug: "24-spaces-create-modal", view: "wiki-sidebar", section: null, openCreateSpaceModal: true },
+];
+
+const mobileTargets = desktopTargets
+  .filter((target) => !target.openCreateSpaceModal)
+  .map((target) => ({
+    ...target,
+    slug: `mobile/${target.slug}`,
+    // In the production host, the route sidebar lives in the mobile drawer.
+    // The page body should therefore be checked without the desktop sidebar.
+    view: target.view === "wiki-sidebar" ? "wiki" : target.view,
+    viewport: mobileViewport,
+  }));
+
+const targets = [
+  ...desktopTargets.map((target) => ({ ...target, viewport: desktopViewport })),
+  ...mobileTargets,
+];
+
+const playwrightUrl = pathToFileURL(resolve(pkgRoot, "node_modules/playwright/index.mjs")).href;
+const playwrightFallback = resolve(pkgRoot, "..", "..", "..", "node_modules", ".pnpm", "playwright@1.58.2", "node_modules", "playwright", "index.mjs");
+let playwrightModuleHref = playwrightUrl;
+if (!existsSync(resolve(pkgRoot, "node_modules/playwright/index.mjs"))) {
+  if (existsSync(playwrightFallback)) {
+    playwrightModuleHref = pathToFileURL(playwrightFallback).href;
+  } else {
+    throw new Error("Cannot locate playwright module");
+  }
+}
+const { chromium } = await import(playwrightModuleHref);
+
+const mimeFor = (ext) => ({
+  ".html": "text/html; charset=utf-8",
+  ".js": "application/javascript; charset=utf-8",
+  ".mjs": "application/javascript; charset=utf-8",
+  ".css": "text/css; charset=utf-8",
+  ".map": "application/json; charset=utf-8",
+})[ext] ?? "application/octet-stream";
+
+const server = http.createServer((req, res) => {
+  const url = new URL(req.url ?? "/", "http://localhost");
+  const requestedPath = url.pathname === "/" ? "/index.html" : url.pathname;
+  const ext = extname(requestedPath);
+  const candidate = ext ? resolve(outDir, "." + requestedPath) : resolve(outDir, "./index.html");
+  try {
+    const body = readFileSync(candidate);
+    res.writeHead(200, { "Content-Type": mimeFor(extname(candidate)) });
+    res.end(body);
+  } catch {
+    res.writeHead(404);
+    res.end("Not found: " + candidate);
+  }
+});
+await new Promise((r) => server.listen(0, "127.0.0.1", r));
+const { port } = server.address();
+const baseUrl = `http://127.0.0.1:${port}`;
+
+const browser = await chromium.launch({ headless: true });
+const context = await browser.newContext({ viewport: desktopViewport, deviceScaleFactor: 2 });
+const page = await context.newPage();
+page.on("console", (msg) => console.log(`  [console.${msg.type()}]`, msg.text()));
+page.on("pageerror", (err) => console.error("  [pageerror]", err.message));
+
+for (const target of targets) {
+  const sectionPath = target.section ? `/${target.section}` : "";
+  const search = target.search ? `?${target.search}` : "";
+  const url = `${baseUrl}/PAP/wiki${sectionPath}${search}#${target.view}`;
+  console.log(`→ rendering ${target.slug} (${url})`);
+  await page.setViewportSize(target.viewport);
+  await page.goto(url, { waitUntil: "networkidle" });
+  await page.waitForTimeout(200);
+  if (target.slug === "09-sidebar-link") {
+    await page.addStyleTag({ content: "body { background: var(--sidebar); }" });
+  }
+  if (target.openCreateSpaceModal) {
+    await page.evaluate(() => {
+      const btn = document.querySelector('button[aria-label="Create space"]');
+      if (!btn) throw new Error("Create space button not found in DOM");
+      (btn).click();
+    });
+    await page.waitForSelector('[aria-labelledby="create-space-modal-title"]', { timeout: 5000 });
+    await page.waitForTimeout(150);
+  }
+  if (target.scrollToText) {
+    await page.getByText(target.scrollToText).first().scrollIntoViewIfNeeded();
+    await page.waitForTimeout(100);
+  }
+  const outFile = resolve(screensDir, `${target.slug}.png`);
+  mkdirSync(dirname(outFile), { recursive: true });
+  await page.screenshot({ path: outFile, fullPage: false });
+  const horizontalOverflow = await page.evaluate(() => {
+    const rootOverflow = document.documentElement.scrollWidth - document.documentElement.clientWidth;
+    const bodyOverflow = document.body.scrollWidth - window.innerWidth;
+    return Math.max(rootOverflow, bodyOverflow);
+  });
+  if (horizontalOverflow > 1) {
+    throw new Error(`${target.slug} has ${horizontalOverflow}px horizontal overflow at ${target.viewport.width}px`);
+  }
+  console.log(`  saved ${outFile}`);
+}
+
+await browser.close();
+server.close();
+console.log("Done. Screenshots in", screensDir);

packages/plugins/plugin-llm-wiki/tests/screenshots/entry.tsx

@@ -0,0 +1,6 @@
+import { createRoot } from "react-dom/client";
+import { App } from "./harness.js";
+
+const container = document.getElementById("root");
+if (!container) throw new Error("No #root in harness host");
+createRoot(container).render(<App />);

packages/plugins/plugin-llm-wiki/tests/screenshots/index.html

@@ -0,0 +1,84 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <title>LLM Wiki UI Harness</title>
+    <style>
+      :root {
+        --background: oklch(0.145 0 0);
+        --foreground: oklch(0.985 0 0);
+        --card: oklch(0.205 0 0);
+        --primary: oklch(0.985 0 0);
+        --primary-foreground: oklch(0.205 0 0);
+        --secondary: oklch(0.269 0 0);
+        --secondary-foreground: oklch(0.985 0 0);
+        --muted: oklch(0.269 0 0);
+        --muted-foreground: oklch(0.708 0 0);
+        --accent: oklch(0.269 0 0);
+        --accent-foreground: oklch(0.985 0 0);
+        --border: oklch(0.269 0 0);
+        --input: oklch(0.269 0 0);
+        --sidebar: oklch(0.145 0 0);
+      }
+      html, body, #root {
+        margin: 0;
+        padding: 0;
+        height: 100%;
+        background: var(--background);
+        color: var(--foreground);
+        font-family: ui-sans-serif, system-ui, -apple-system, "Segoe UI", Roboto, sans-serif;
+        font-size: 14px;
+      }
+
+      /* Minimal Tailwind utility shim — supports just the classes used by the */
+      /* plugin's WikiRouteSidebar so the screenshot harness renders something */
+      /* visually close to the production host (which compiles real Tailwind). */
+      .w-60 { width: 15rem; }
+      .h-full { height: 100%; }
+      .min-h-0 { min-height: 0; }
+      .border-r { border-right-width: 1px; border-right-style: solid; }
+      .border-t { border-top-width: 1px; border-top-style: solid; }
+      .border-border { border-color: var(--border); }
+      .bg-background { background: var(--background); }
+      .bg-accent { background: var(--accent); }
+      .flex { display: flex; }
+      .flex-col { flex-direction: column; }
+      .flex-1 { flex: 1; }
+      .items-center { align-items: center; }
+      .gap-0\.5 { gap: 0.125rem; }
+      .gap-1 { gap: 0.25rem; }
+      .gap-1\.5 { gap: 0.375rem; }
+      .gap-2 { gap: 0.5rem; }
+      .gap-2\.5 { gap: 0.625rem; }
+      .mb-2 { margin-bottom: 0.5rem; }
+      .mb-3 { margin-bottom: 0.75rem; }
+      .px-2 { padding-left: 0.5rem; padding-right: 0.5rem; }
+      .px-3 { padding-left: 0.75rem; padding-right: 0.75rem; }
+      .py-1 { padding-top: 0.25rem; padding-bottom: 0.25rem; }
+      .py-1\.5 { padding-top: 0.375rem; padding-bottom: 0.375rem; }
+      .py-2 { padding-top: 0.5rem; padding-bottom: 0.5rem; }
+      .py-3 { padding-top: 0.75rem; padding-bottom: 0.75rem; }
+      .shrink-0 { flex-shrink: 0; }
+      .text-xs { font-size: 0.75rem; line-height: 1rem; }
+      .text-sm { font-size: 0.875rem; line-height: 1.25rem; }
+      .text-\[11px\] { font-size: 11px; }
+      .text-\[13px\] { font-size: 13px; }
+      .font-medium { font-weight: 500; }
+      .font-semibold { font-weight: 600; }
+      .font-bold { font-weight: 700; }
+      .uppercase { text-transform: uppercase; }
+      .tracking-normal { letter-spacing: 0; }
+      .text-foreground { color: var(--foreground); }
+      .text-foreground\/80 { color: color-mix(in oklab, var(--foreground) 80%, transparent); }
+      .text-muted-foreground { color: var(--muted-foreground); }
+      .truncate { overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
+      .rounded-md { border-radius: 0.375rem; }
+      .transition-colors { transition: background-color 150ms, color 150ms; }
+      .overflow-y-auto { overflow-y: auto; }
+    </style>
+  </head>
+  <body>
+    <div id="root"></div>
+    <script type="module" src="/bundle.js"></script>
+  </body>
+</html>