docs: hide CLI, Scaffold, and Hyperboards pages

components/Layout.js

@@ -163,7 +163,7 @@ export default function Layout({ children, frontmatter }) {
           <span className="header-divider" aria-hidden="true" />
           <nav className="header-nav" aria-label="Main navigation">
             <Link href="/getting-started/quickstart" className="header-nav-link">Docs</Link>
-            <Link href="/tools/scaffold" className="header-nav-link">Tools</Link>
+            <Link href="/tools/hypercerts-agent-skills" className="header-nav-link">Tools</Link>
           </nav>
           <div style={{ flex: 1 }} />
           <button

components/SearchDialog.js

@@ -26,7 +26,6 @@ const QUICK_LINK_PATHS = [
   '/getting-started/quickstart',
   '/core-concepts/what-is-hypercerts',
   '/core-concepts/hypercerts-core-data-model',
-  '/tools/scaffold',
   '/architecture/overview',
   '/reference/glossary',
 ];

lib/generate-search-index.js

@@ -1,5 +1,6 @@
 const { readdirSync, statSync, readFileSync, writeFileSync } = require("fs");
 const { join, relative } = require("path");
+const { hiddenPaths } = require("./page-visibility.json");
 const {
   loadExternalDocsContent,
   parseMarkdownFrontmatter,
@@ -9,6 +10,7 @@ const {
 const PAGES_DIR = join(__dirname, "..", "pages");
 const OUTPUT = join(__dirname, "..", "public", "search-index.json");
 const MAX_BODY_LENGTH = 5000;
+const HIDDEN_PATHS = new Set(hiddenPaths);
 
 function walkDir(dir) {
   const results = [];
@@ -111,6 +113,8 @@ async function main() {
     const rel = "/" + relative(PAGES_DIR, file).replace(/\.md$/, "");
     const path = rel === "/index" ? "/" : rel;
 
+    if (HIDDEN_PATHS.has(path)) continue;
+
     const frontmatter = parseMarkdownFrontmatter(localContent, relative(PAGES_DIR, file));
     const title = getStringFrontmatterValue(frontmatter, "title");
     const description = getStringFrontmatterValue(frontmatter, "description");

lib/generate-sitemap.js

@@ -1,7 +1,9 @@
 const fs = require('fs');
 const path = require('path');
+const { hiddenPaths } = require('./page-visibility.json');
 
 const SITE_URL = 'https://docs.hypercerts.org';
+const HIDDEN_PATHS = new Set(hiddenPaths);
 
 function getPages(dir, base = '') {
   const entries = fs.readdirSync(dir, { withFileTypes: true });
@@ -26,7 +28,7 @@ function getPages(dir, base = '') {
 
 function generateSitemap() {
   const pagesDir = path.join(__dirname, '..', 'pages');
-  const pages = getPages(pagesDir);
+  const pages = getPages(pagesDir).filter((page) => !HIDDEN_PATHS.has(page));
 
   const today = new Date().toISOString().split('T')[0];
 

lib/navigation.js

@@ -60,12 +60,9 @@ export const navigation = [
   {
     section: "Tools",
     children: [
-      { title: "Scaffold Starter App", path: "/tools/scaffold" },
-      { title: "Hypercerts CLI", path: "/tools/hypercerts-cli" },
       { title: "Agent Skills", path: "/tools/hypercerts-agent-skills" },
       { title: "Hyperindex", path: "/tools/hyperindex" },
       { title: "Hyperscan", path: "/tools/hyperscan" },
-      { title: "Hyperboards", path: "/tools/hyperboards" },
       { title: "Labelers", path: "/tools/labelers" },
     ],
   },

lib/page-visibility.json

@@ -0,0 +1,7 @@
+{
+  "hiddenPaths": [
+    "/tools/hypercerts-cli",
+    "/tools/scaffold",
+    "/tools/hyperboards"
+  ]
+}

pages/architecture/account-and-identity.md

@@ -90,7 +90,7 @@ See [ePDS (extended PDS)](/architecture/epds) for integration examples, handle m
 
 For scripts, CLI tools, and server-side automation, use app passwords instead of your main password. App passwords are scoped credentials that can be revoked independently.
 
-Create one in your account settings at [certified.app](https://certified.app). Give it a descriptive name (e.g., "CI/CD pipeline" or "Local development"). If a credential is compromised, revoke just that app password — your main account stays secure. The [Hypercerts CLI](/tools/hypercerts-cli) uses app passwords for authentication.
+Create one in your account settings at [certified.app](https://certified.app). Give it a descriptive name (e.g., "CI/CD pipeline" or "Local development"). If a credential is compromised, revoke just that app password — your main account stays secure.
 
 {% callout type="warning" %}
 Never commit app passwords to version control. Use environment variables or a secrets manager.

pages/getting-started/quickstart.md

@@ -64,7 +64,7 @@ const { session } = await client.callback(new URLSearchParams(callbackQuery));
 const agent = new Agent(session);
 ```
 
-See the [AT Protocol OAuth documentation](https://atproto.com/specs/oauth) for full details on client metadata, session storage, and keyset configuration. For further info on how to set up OAuth you can check out [AT Protos node.js implementation tutorial](https://atproto.com/guides/oauth-cli-tutorial) or the [scaffold app](/tools/scaffold).
+See the [AT Protocol OAuth documentation](https://atproto.com/specs/oauth) for full details on client metadata, session storage, and keyset configuration. For a step-by-step Node.js example, see the [AT Protocol OAuth tutorial](https://atproto.com/guides/oauth-cli-tutorial).
 
 ## Create your first hypercert
 
@@ -347,8 +347,6 @@ Your hypercert is now created and stored on your PDS. The completion screen show
 ![Completion screen showing the finished hypercert](/images/scaffold/finalized-cert.png)
 *The hypercert is created and stored on your PDS.*
 
-For full details on the Scaffold app — including self-hosting, environment setup, and extending the codebase — see the [Scaffold app documentation](/tools/scaffold).
-
 ## Next steps
 
 Third parties can now [evaluate your hypercert](/getting-started/working-with-evaluations) by creating evaluation records and measurements on their own PDS.

pages/tools/hyperscan.md

@@ -124,5 +124,4 @@ Use the Agent API when you want a tool, bot, or coding agent to understand the c
 
 - [Hyperindex](/tools/hyperindex) — indexer used to query and serve indexed Hypercerts data
 - [Labelers](/tools/labelers) — ATProto label services used for quality and trust signals
-- [Hypercerts CLI](/tools/hypercerts-cli) — command-line tool for creating and inspecting Hypercerts records
 - [Introduction to Lexicons](/lexicons/introduction-to-lexicons) — schemas behind the records shown in Hyperscan

test/hidden-tool-visibility.test.js

@@ -0,0 +1,69 @@
+const assert = require('node:assert/strict');
+const { execFileSync } = require('node:child_process');
+const { existsSync, readFileSync, readdirSync } = require('node:fs');
+const { join, relative } = require('node:path');
+const test = require('node:test');
+
+const ROOT = join(__dirname, '..');
+const PAGES_DIR = join(ROOT, 'pages');
+const HIDDEN_PATHS = [
+  '/tools/hypercerts-cli',
+  '/tools/scaffold',
+  '/tools/hyperboards',
+];
+const HIDDEN_PAGE_FILES = new Set(HIDDEN_PATHS.map((path) => `pages${path}.md`));
+
+function walkMarkdownFiles(directory) {
+  return readdirSync(directory, { withFileTypes: true }).flatMap((entry) => {
+    const path = join(directory, entry.name);
+    return entry.isDirectory() ? walkMarkdownFiles(path) : path.endsWith('.md') ? [path] : [];
+  });
+}
+
+test('keeps the hidden tool page source files', () => {
+  for (const file of HIDDEN_PAGE_FILES) {
+    assert.equal(existsSync(join(ROOT, file)), true, `${file} must remain available for direct routes`);
+  }
+});
+
+test('excludes hidden tool pages from the generated search index', () => {
+  execFileSync(process.execPath, ['lib/generate-search-index.js'], { cwd: ROOT });
+  const index = JSON.parse(readFileSync(join(ROOT, 'public/search-index.json'), 'utf8'));
+  const indexedHiddenPaths = index
+    .map((page) => page.path)
+    .filter((path) => HIDDEN_PATHS.includes(path));
+
+  assert.deepEqual(indexedHiddenPaths, []);
+});
+
+test('excludes hidden tool pages from the generated sitemap', () => {
+  execFileSync(process.execPath, ['lib/generate-sitemap.js'], { cwd: ROOT });
+  const sitemap = readFileSync(join(ROOT, 'public/sitemap.xml'), 'utf8');
+
+  for (const path of HIDDEN_PATHS) {
+    assert.doesNotMatch(sitemap, new RegExp(`<loc>[^<]+${path}</loc>`));
+  }
+});
+
+test('does not link to hidden tool pages from visible documentation or navigation', () => {
+  const authoredFiles = [
+    join(ROOT, 'components/Layout.js'),
+    join(ROOT, 'components/SearchDialog.js'),
+    join(ROOT, 'lib/navigation.js'),
+    ...walkMarkdownFiles(PAGES_DIR).filter((file) => {
+      const repoPath = relative(ROOT, file).split('\\').join('/');
+      return !HIDDEN_PAGE_FILES.has(repoPath);
+    }),
+  ];
+
+  for (const file of authoredFiles) {
+    const content = readFileSync(file, 'utf8');
+    for (const path of HIDDEN_PATHS) {
+      assert.equal(
+        content.includes(path),
+        false,
+        `${relative(ROOT, file)} still links to ${path}`,
+      );
+    }
+  }
+});