diff --git a/docs/build_docs.py b/docs/build_docs.py
index a846551..6a31034 100644
--- a/docs/build_docs.py
+++ b/docs/build_docs.py
@@ -12,11 +12,11 @@
 import tomllib
 from datetime import datetime
 from fnmatch import fnmatchcase
-from html import escape
+from html import escape, unescape
 from html.parser import HTMLParser
 from importlib import import_module
 from pathlib import Path
-from urllib.parse import urljoin
+from urllib.parse import urljoin, urlsplit
 from xml.etree import ElementTree
 
 import jupytext
@@ -318,6 +318,239 @@ def sitemap_last_modified(html: Path, doctrees: Path) -> dict[str, str]:
     }
 
 
+def navigation_head_html() -> str:
+    return """<link rel="preload" as="font" href="https://docs.nygen.io/assets/brand/fonts/inter/latin.woff2" type="font/woff2" crossorigin/>
+<script>
+(() => {
+  const observer = new MutationObserver(() => {
+    if (!document.querySelector('main')) return;
+    observer.disconnect();
+    const sidebar = document.querySelector('.myst-primary-sidebar-nav');
+    const home = document.querySelector('.myst-home-link');
+    if (sidebar?.clientHeight && home) {
+      const saved = sessionStorage.getItem('nygen-docs-sidebar:' + home.pathname);
+      if (saved !== null) sidebar.scrollTop = Number(saved);
+    }
+  });
+  observer.observe(document.documentElement, {childList: true, subtree: true});
+})();
+</script>
+<script defer src="https://docs.nygen.io/assets/brand/docs.js"></script>"""
+
+
+def html_fragment(contents: str, class_name: str) -> str:
+    class Fragment(HTMLParser):
+        def __init__(self) -> None:
+            super().__init__()
+            self.lines = [0, *(match.end() for match in re.finditer("\n", contents))]
+            self.depth = 0
+            self.start = 0
+            self.matches: list[str] = []
+
+        def position(self) -> int:
+            line, column = self.getpos()
+            return self.lines[line - 1] + column
+
+        def handle_starttag(
+            self, tag: str, attrs: list[tuple[str, str | None]]
+        ) -> None:
+            if self.depth:
+                self.depth += tag not in ArticleText.void_tags
+            elif class_name in (dict(attrs).get("class") or "").split():
+                self.start = self.position()
+                self.depth = 1
+
+        def handle_startendtag(
+            self, tag: str, attrs: list[tuple[str, str | None]]
+        ) -> None:
+            pass
+
+        def handle_endtag(self, tag: str) -> None:
+            if not self.depth:
+                return
+            self.depth -= 1
+            if not self.depth:
+                end = contents.index(">", self.position()) + 1
+                self.matches.append(contents[self.start : end])
+
+    parser = Fragment()
+    parser.feed(contents)
+    if parser.depth or len(parser.matches) != 1:
+        raise ValueError(f"Expected one complete .{class_name} element")
+    return parser.matches[0]
+
+
+def include_api_navigation(site: Path) -> None:
+    base_url = os.environ.get("BASE_URL", "").rstrip("/")
+    source = DOCS / "build" / "api" / "index.html"
+    navigation = html_fragment(source.read_text(), "docs-api-tree")
+    links = []
+    for href, title in re.findall(
+        r'<a\b[^>]*\bhref="([^"]+)"[^>]*>(.*?)</a>', navigation, re.DOTALL
+    ):
+        href = unescape(href)
+        if urlsplit(href).scheme or href.startswith("//") or not href.endswith(".html"):
+            raise ValueError(f"Expected an API page link in {source}: {href}")
+        links.append(
+            {
+                "title": " ".join(unescape(re.sub(r"<[^>]+>", "", title)).split()),
+                "url": urljoin(f"{base_url}/api/", href),
+                "open_in_same_tab": True,
+            }
+        )
+    if not links:
+        raise ValueError(f"No API navigation links in {source}")
+    config = yaml.safe_load((site / "myst.yml").read_text())
+    entries = list(config["project"]["toc"])
+    matches = []
+    while entries:
+        entry = entries.pop()
+        if entry.get("url") == f"{base_url}/api/index.html":
+            matches.append(entry)
+        entries.extend(entry.get("children", []))
+    if len(matches) != 1:
+        raise ValueError(f"Expected one API reference entry in {site / 'myst.yml'}")
+    matches[0]["children"] = links
+    (site / "myst.yml").write_text(yaml.safe_dump(config, sort_keys=False))
+
+
+def integrate_api_navigation(html: Path) -> None:
+    def static_classes(match: re.Match[str]) -> str:
+        classes = [
+            token
+            for token in match[1].split()
+            if (
+                token.startswith("myst-")
+                or token in {"collapsible-content", "sr-only", "hide-mac", "show-mac"}
+            )
+            and token not in {"myst-toc-item-exact", "myst-search-bar-disabled"}
+        ]
+        if "myst-search-bar" in classes:
+            classes.append("search-button__button")
+        if "myst-top-nav-menu-button" in classes:
+            classes.extend(("sidebar-toggle", "primary-toggle"))
+        return f'class="{" ".join(classes)}"'
+
+    home = (html / "index.html").read_text()
+    header = html_fragment(home, "myst-top-nav-bar")
+    header = re.sub(r"<script\b[^>]*>.*?</script>", "", header, flags=re.DOTALL)
+    header = re.sub(r'\bclass="([^"]*)"', static_classes, header)
+    header, count = re.subn(
+        r'<button\b[^>]*\bclass="[^"]*\bmyst-search-bar\b[^"]*"[^>]*>',
+        lambda match: (
+            re.sub(
+                r' (?:aria-expanded|data-state|aria-label|aria-controls)="[^"]*"',
+                "",
+                match[0][:-1],
+            )
+            + ' aria-label="Search documentation" aria-controls="pst-search-dialog">'
+        ),
+        header,
+    )
+    if count != 1:
+        raise ValueError("Expected one MyST search button in the guide header")
+    navigation = html_fragment(home, "myst-primary-sidebar-toc")
+    navigation = re.sub(r' aria-current="[^"]*"', "", navigation)
+    navigation = re.sub(r'\bclass="([^"]*)"', static_classes, navigation)
+    base_url = os.environ.get("BASE_URL", "").rstrip("/")
+    for page in (html / "api").glob("*.html"):
+        contents = page.read_text()
+        route = f"{base_url}/{page.relative_to(html).as_posix()}"
+
+        def mark_current(match: re.Match[str]) -> str:
+            tag = match[0]
+            href = re.search(r'\bhref="([^"]+)"', tag)
+            return (
+                tag[:-1] + ' aria-current="page">'
+                if href and unescape(href[1]) == route
+                else tag
+            )
+
+        current_navigation = re.sub(r"<a\b[^>]*>", mark_current, navigation)
+        contents = contents.replace(
+            html_fragment(contents, "docs-header-placeholder"), header
+        )
+        contents = contents.replace(
+            html_fragment(contents, "docs-api-tree"), current_navigation
+        )
+        if contents.count("</head>") != 1:
+            raise ValueError(f"Expected one HTML head in {page}")
+        page.write_text(
+            contents.replace("</head>", navigation_head_html() + "</head>", 1)
+        )
+
+
+def update_page_metadata(contents: str, canonical: str) -> str:
+    class Description(HTMLParser):
+        def __init__(self) -> None:
+            super().__init__()
+            self.values: list[str] = []
+
+        def handle_starttag(
+            self, tag: str, attrs: list[tuple[str, str | None]]
+        ) -> None:
+            attributes = dict(attrs)
+            if tag == "meta" and attributes.get("name") == "description":
+                self.values.append(attributes.get("content") or "")
+
+    if contents.count("</head>") != 1:
+        raise ValueError(f"Expected one HTML head for {canonical}")
+    head, body = contents.split("</head>", 1)
+    titles = re.findall(r"<title>(.*?)</title>", head, re.DOTALL)
+    description = Description()
+    description.feed(head)
+    if len(titles) != 1 or len(description.values) != 1 or not description.values[0]:
+        raise ValueError(f"Expected a title and description for {canonical}")
+    title = unescape(titles[0])
+    tool = PUBLIC_URL.rsplit("/", 1)[-1]
+    parts = re.split(r" (?:-|—) ", title)
+    if len(parts) == 2 and (
+        parts[0] == parts[1]
+        or canonical == f"{PUBLIC_URL}/api/index.html"
+        and parts[1] == f"{tool} API reference"
+    ):
+        title = parts[0]
+    if canonical == f"{PUBLIC_URL}/" and title == tool:
+        title = f"{tool} documentation"
+    if (
+        canonical == f"{PUBLIC_URL}/api/{tool.lower()}.html"
+        and title == f"{tool} API reference"
+    ):
+        title = f"{tool} Python API"
+    image = f"https://docs.nygen.io/assets/brand/logo/{tool.lower()}-dark.png"
+    metadata = {
+        "og:title": title,
+        "og:description": description.values[0],
+        "og:type": "website",
+        "og:url": canonical,
+        "og:image": image,
+        "og:image:type": "image/png",
+        "og:image:width": "512",
+        "og:image:height": "512",
+        "og:image:alt": f"{tool} logo",
+        "twitter:card": "summary",
+        "twitter:image": image,
+        "twitter:image:alt": f"{tool} logo",
+    }
+
+    def remove_managed(match: re.Match[str]) -> str:
+        key = re.search(r"""\b(?:name|property)=["']([^"']+)["']""", match[0])
+        return "" if key and key[1] in metadata else match[0]
+
+    head = re.sub(r"<meta\b[^>]*>", remove_managed, head)
+    head = re.sub(
+        r"<title>.*?</title>",
+        lambda _: f"<title>{escape(title)}</title>",
+        head,
+        count=1,
+        flags=re.DOTALL,
+    )
+    for name, value in metadata.items():
+        attribute = "property" if name.startswith("og:") else "name"
+        head += f'<meta {attribute}="{name}" content="{escape(value, quote=True)}"/>'
+    return head + "</head>" + body
+
+
 def write_discovery_files(
     html: Path,
     api_text: Path,
@@ -381,7 +614,7 @@ def write_discovery_files(
         page = html / route.lstrip("/")
         if route.endswith("/"):
             page /= "index.html"
-        contents = page.read_text()
+        contents = update_page_metadata(page.read_text(), canonical)
         canonical_tag = (
             f'<link rel="canonical" href="{escape(canonical, quote=True)}"/>'
         )
@@ -392,28 +625,7 @@ def write_discovery_files(
             f'<link rel="alternate" type="text/plain" href="{base_url}/{export}"/>'
         )
         if route.endswith("/"):
-            script_url = "https://docs.nygen.io/assets/brand/docs.js"
-            links += (
-                '<link rel="preload" as="font" '
-                'href="https://docs.nygen.io/assets/brand/fonts/inter/latin.woff2" '
-                'type="font/woff2" crossorigin/>'
-            )
-            links += """<script>
-(() => {
-  const observer = new MutationObserver(() => {
-    if (!document.querySelector('main')) return;
-    observer.disconnect();
-    const sidebar = document.querySelector('.myst-primary-sidebar-nav');
-    const home = document.querySelector('.myst-home-link');
-    if (sidebar?.clientHeight && home) {
-      const saved = sessionStorage.getItem('nygen-docs-sidebar:' + home.pathname);
-      if (saved !== null) sidebar.scrollTop = Number(saved);
-    }
-  });
-  observer.observe(document.documentElement, {childList: true, subtree: true});
-})();
-</script>"""
-            links += f'<script defer src="{script_url}"></script>'
+            links += navigation_head_html()
         if not count:
             links = canonical_tag + links
         if contents.count("</head>") != 1:
@@ -730,29 +942,47 @@ def prepare_site_template(site: Path) -> None:
             check=True,
         )
     replacements = {
-        "build/index.js": (
-            'Pje.default.useState(i);(0,Pje.useEffect)(()=>{o.state==="idle"'
-            "&&s(tzt([t],e,r).includes(t.id))}",
-            'Pje.default.useState(!0);(0,Pje.useEffect)(()=>{o.state==="idle"&&s(!0)}',
-        ),
-        "public/build/_shared/chunk-LS4ALTVG.js": (
-            '_0.default.useState(o);(0,_0.useEffect)(()=>{i.state==="idle"'
-            "&&a(DS([t],e,r).includes(t.id))}",
-            '_0.default.useState(!0);(0,_0.useEffect)(()=>{i.state==="idle"&&a(!0)}',
-        ),
+        "build/index.js": [
+            (
+                'Pje.default.useState(i);(0,Pje.useEffect)(()=>{o.state==="idle"'
+                "&&s(tzt([t],e,r).includes(t.id))}",
+                'Pje.default.useState(!0);(0,Pje.useEffect)(()=>{o.state==="idle"&&s(!0)}',
+            ),
+            (
+                'title:o!=null&&o.title?`${o.title}${a?` - ${a}`:""}`:a',
+                'title:o!=null&&o.title?o.title===a?`${a} documentation`:`${o.title}${a?` - ${a}`:""}`:a',
+            ),
+        ],
+        "public/build/_shared/chunk-LS4ALTVG.js": [
+            (
+                '_0.default.useState(o);(0,_0.useEffect)(()=>{i.state==="idle"'
+                "&&a(DS([t],e,r).includes(t.id))}",
+                '_0.default.useState(!0);(0,_0.useEffect)(()=>{i.state==="idle"&&a(!0)}',
+            ),
+        ],
+        "public/build/_shared/chunk-WGW5MSUV.js": [
+            (
+                'title:m!=null&&m.title?`${m.title}${g?` - ${g}`:""}`:g',
+                'title:m!=null&&m.title?m.title===g?`${g} documentation`:`${m.title}${g?` - ${g}`:""}`:g',
+            ),
+        ],
     }
     fingerprint = hashlib.sha256(
         json.dumps(replacements, sort_keys=True).encode()
     ).hexdigest()[:12]
-    for filename, (original, expanded) in replacements.items():
+    for filename, rules in replacements.items():
         path = template / filename
         if not path.is_file() and filename.startswith("public/"):
-            path = path.with_stem(f"{path.stem}-{fingerprint}")
-        content = path.read_text()
-        if content.count(original) == 1 and expanded not in content:
-            path.write_text(content.replace(original, expanded))
-        elif original in content or content.count(expanded) != 1:
-            raise ValueError(f"Unexpected navigation component in {path}")
+            matches = list(path.parent.glob(f"{path.stem}-*.js"))
+            if len(matches) != 1:
+                raise ValueError(f"Expected one cached theme module for {path}")
+            path = matches[0]
+        for original, replacement in rules:
+            content = path.read_text()
+            if content.count(original) == 1 and replacement not in content:
+                path.write_text(content.replace(original, replacement))
+            elif original in content or content.count(replacement) != 1:
+                raise ValueError(f"Unexpected theme component in {path}")
     modules = list((template / "public" / "build").rglob("*.js"))
     filenames = {
         path.name: f"{path.stem}-{fingerprint}.js"
@@ -784,12 +1014,18 @@ def main() -> None:
     )
     args = parser.parse_args()
     site = prepare_site(preview=args.preview)
+    include_api_navigation(site)
     prepare_site_template(site)
     subprocess.run(
         ["myst", "build", "--html", "--strict"],
         cwd=site,
         check=True,
     )
+    shutil.copytree(
+        DOCS / "build" / "api",
+        SITE / "_build" / "html" / "api",
+        ignore=shutil.ignore_patterns(".buildinfo", ".doctrees"),
+    )
     revision = subprocess.run(
         ["git", "describe", "--always", "--dirty", "--abbrev=40"],
         cwd=DOCS.parent,
@@ -806,6 +1042,7 @@ def main() -> None:
         ),
     )
     link_shared_brand_assets(SITE / "_build" / "html")
+    integrate_api_navigation(SITE / "_build" / "html")
 
 
 if __name__ == "__main__":
diff --git a/docs/source/myst.yml b/docs/source/myst.yml
index e09c250..43169d4 100644
--- a/docs/source/myst.yml
+++ b/docs/source/myst.yml
@@ -12,7 +12,6 @@ project:
   - reference/api/**
   static_files:
   - llms.txt
-  - ../build/api
   toc:
   - file: index.md
   - title: Getting started
diff --git a/docs/source/reference/api/_templates/docs-navigation.html b/docs/source/reference/api/_templates/docs-navigation.html
new file mode 100644
index 0000000..4c7d26a
--- /dev/null
+++ b/docs/source/reference/api/_templates/docs-navigation.html
@@ -0,0 +1,5 @@
+<div class="myst-primary-sidebar-nav docs-api-navigation">
+  <nav class="docs-api-tree" aria-label="API reference">
+    {{ generate_toctree_html(startdepth=0, kind="sidebar", maxdepth=1, collapse=False, includehidden=True, titles_only=True, show_nav_level=1) }}
+  </nav>
+</div>
diff --git a/docs/source/reference/api/_templates/layout.html b/docs/source/reference/api/_templates/layout.html
new file mode 100644
index 0000000..3f76d10
--- /dev/null
+++ b/docs/source/reference/api/_templates/layout.html
@@ -0,0 +1,29 @@
+{% extends "sphinx_book_theme/layout.html" %}
+
+{% block extrahead %}
+{{ super() }}
+{% if pagename == "search" %}<meta name="robots" content="noindex,follow"/>{% endif %}
+{% endblock %}
+
+{% block css %}
+<script>
+(() => {
+  const theme = localStorage.getItem('myst:theme') ?? (matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light');
+  localStorage.setItem('mode', theme);
+  localStorage.setItem('theme', theme);
+  document.documentElement.dataset.theme = theme;
+  document.documentElement.classList.add(theme);
+})();
+</script>
+{{ super() }}
+{% endblock %}
+
+{% block body_tag %}
+<body class="docs-api" data-default-mode="{{ default_mode }}">
+{% endblock %}
+
+{% block docs_navbar %}
+<header id="pst-header" class="bd-header myst-top-nav docs-api-top-nav">
+  <nav class="docs-header-placeholder"></nav>
+</header>
+{% endblock %}
diff --git a/docs/source/reference/api/conf.py b/docs/source/reference/api/conf.py
index b8ac098..2e854b4 100644
--- a/docs/source/reference/api/conf.py
+++ b/docs/source/reference/api/conf.py
@@ -25,6 +25,8 @@
 language = "en"
 
 html_theme = "sphinx_book_theme"
+templates_path = ["_templates"]
+html_sidebars = {"**": ["docs-navigation.html"]}
 html_css_files = ["https://docs.nygen.io/assets/brand/docs.css"]
 html_logo = "https://docs.nygen.io/assets/brand/logo/cytebase.svg"
 html_favicon = "https://docs.nygen.io/assets/brand/logo/cytebase.ico"
@@ -34,7 +36,11 @@
     "logo": {"text": "CyteBase", "alt_text": "CyteBase"},
     "repository_url": "https://github.com/NygenAnalytics/CyteBase",
     "path_to_docs": "docs/source/reference/api",
-    "use_repository_button": True,
+    "article_header_start": [],
+    "article_header_end": ["toggle-secondary-sidebar.html"],
+    "show_prev_next": False,
+    "footer_content_items": ["extra-footer.html"],
+    "extra_footer": '<a class="docs-home-link" href="https://docs.nygen.io/"><img class="brand-symbol" src="https://docs.nygen.io/assets/brand/logo/nygen-symbol.svg" alt="Nygen documentation home" width="32" height="32"></a>',
     "show_navbar_depth": 2,
     "navigation_with_keys": False,
 }
diff --git a/tests/test_docs_render.py b/tests/test_docs_render.py
index f9aa778..eaf35ab 100644
--- a/tests/test_docs_render.py
+++ b/tests/test_docs_render.py
@@ -610,7 +610,7 @@ def rendered_discovery_files(
         page = html / route.strip("/") / "index.html"
         page.parent.mkdir(parents=True, exist_ok=True)
         page.write_text(
-            f"<html><head><title>{name}</title></head>"
+            f'<html><head><title>{name}</title><meta name="description" content="Authored guide description."/></head>'
             f"<body><nav>Site navigation</nav><article><h1>{name}</h1>"
             "<p>Saved result: 42 cells.</p>"
             "<pre>def count():\n    return 42\n\nprint(count())\n42</pre>"
@@ -643,7 +643,9 @@ def rendered_discovery_files(
         "# CyteBase\n\n```{autoclass} cytebase.Catalog\n:members:\n```\n"
     )
     (html / "api" / "cytebase.html").write_text(
-        '<html><head><link rel="canonical" '
+        "<html><head><title>CyteBase API reference</title>"
+        '<meta name="description" content="Authored API description."/>'
+        '<link rel="canonical" '
         'href="https://docs.nygen.io/CyteBase/api/cytebase.html" /></head>'
         "<body>Catalog(bucket=None, token=None, *, version=None)</body></html>"
     )
@@ -677,6 +679,95 @@ def rendered_discovery_files(
     return html, api_text, base_url
 
 
+@pytest.mark.parametrize(
+    ("route", "title", "expected"),
+    [
+        ("/", "CyteBase - CyteBase", "CyteBase documentation"),
+        ("/quickstart/", "Quick start - CyteBase", "Quick start - CyteBase"),
+        (
+            "/api/index.html",
+            "CyteBase Python API reference — CyteBase API reference",
+            "CyteBase Python API reference",
+        ),
+        (
+            "/api/cytebase.html",
+            "CyteBase API reference — CyteBase API reference",
+            "CyteBase Python API",
+        ),
+    ],
+)
+def test_page_metadata_preserves_authored_content_and_completes_link_previews(
+    route: str, title: str, expected: str
+) -> None:
+    pytest.importorskip("jupytext")
+    pytest.importorskip("nbformat")
+    pytest.importorskip("yaml")
+    from docs import build_docs
+
+    class Metadata(HTMLParser):
+        def __init__(self) -> None:
+            super().__init__()
+            self.tags: list[dict[str, str | None]] = []
+
+        def handle_starttag(
+            self, tag: str, attrs: list[tuple[str, str | None]]
+        ) -> None:
+            if tag == "meta":
+                self.tags.append(dict(attrs))
+
+    body = "<body><h1>Keep this heading</h1><svg><title>Keep SVG title</title></svg></body>"
+    source = (
+        f"<html><head><title>{title}</title>"
+        '<meta name="description" content="Read RNA &amp; ATAC &quot;together&quot;."/>'
+        '<meta property="og:title" content="Stale title"/>'
+        '<meta name="twitter:card" content="summary_large_image"/>'
+        '<meta name="robots" content="noindex,follow"/>'
+        f"</head>{body}</html>"
+    )
+    canonical = build_docs.PUBLIC_URL + route
+
+    actual = build_docs.update_page_metadata(source, canonical)
+
+    head = actual.split("</head>")[0]
+    parser = Metadata()
+    parser.feed(head)
+    keys = [tag.get("property", tag.get("name")) for tag in parser.tags]
+    assert len(keys) == len(set(keys))
+    metadata = dict(zip(keys, (tag["content"] for tag in parser.tags), strict=True))
+    assert re.findall(r"<title>(.*?)</title>", head) == [expected]
+    assert metadata["description"] == 'Read RNA & ATAC "together".'
+    assert metadata["og:description"] == metadata["description"]
+    assert metadata["og:title"] == expected
+    assert metadata["og:type"] == "website"
+    assert metadata["og:url"] == canonical
+    assert (
+        metadata["og:image"]
+        == "https://docs.nygen.io/assets/brand/logo/cytebase-dark.png"
+    )
+    assert metadata["og:image:type"] == "image/png"
+    assert metadata["og:image:width"] == metadata["og:image:height"] == "512"
+    assert metadata["og:image:alt"] == "CyteBase logo"
+    assert metadata["twitter:card"] == "summary"
+    assert metadata["twitter:image"] == metadata["og:image"]
+    assert metadata["twitter:image:alt"] == metadata["og:image:alt"]
+    assert metadata["robots"] == "noindex,follow"
+    assert actual.endswith(body + "</html>")
+    assert build_docs.update_page_metadata(actual, canonical) == actual
+
+
+def test_page_metadata_rejects_missing_authored_description() -> None:
+    pytest.importorskip("jupytext")
+    pytest.importorskip("nbformat")
+    pytest.importorskip("yaml")
+    from docs import build_docs
+
+    with pytest.raises(ValueError, match="Expected a title and description"):
+        build_docs.update_page_metadata(
+            "<html><head><title>Guide</title></head><body></body></html>",
+            build_docs.PUBLIC_URL + "/guide/",
+        )
+
+
 def _discovery_links(page: Path) -> list[dict[str, str | None]]:
     class LinkParser(HTMLParser):
         def __init__(self) -> None:
@@ -1145,3 +1236,160 @@ def test_text_export_preserves_saved_markdown_instead_of_object_repr(
     exported = (html / "quickstart" / "index.txt").read_text()
     assert markdown in exported
     assert "<IPython.core.display.Markdown object>" not in exported
+
+
+@pytest.mark.parametrize("base_url", ["", "/CyteBase"])
+def test_api_pages_join_the_staged_guide_navigation(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch, base_url: str
+) -> None:
+    pytest.importorskip("jupytext")
+    pytest.importorskip("nbformat")
+    yaml = pytest.importorskip("yaml")
+    from docs import build_docs
+
+    api = tmp_path / "docs" / "build" / "api"
+    api.mkdir(parents=True)
+    (api / "index.html").write_text(
+        '<nav class="docs-api-tree"><ul><li>'
+        '<a href="cytebase.html"><span>Catalog API reference</span></a>'
+        '</li><li><a href="import_export.html">Import &amp; export</a>'
+        "</li></ul></nav>"
+    )
+    site = tmp_path / "site"
+    site.mkdir()
+    config = {
+        "project": {
+            "toc": [
+                {"file": "index.md"},
+                {
+                    "title": "Reference",
+                    "children": [
+                        {"url": f"{base_url}/api/index.html", "title": "API reference"}
+                    ],
+                },
+            ]
+        }
+    }
+    (site / "myst.yml").write_text(yaml.safe_dump(config))
+    monkeypatch.setattr(build_docs, "DOCS", api.parents[1])
+    monkeypatch.setenv("BASE_URL", base_url)
+
+    build_docs.include_api_navigation(site)
+
+    toc = yaml.safe_load((site / "myst.yml").read_text())["project"]["toc"]
+    assert toc[0] == {"file": "index.md"}
+    assert toc[1]["children"][0]["children"] == [
+        {
+            "title": "Catalog API reference",
+            "url": f"{base_url}/api/cytebase.html",
+            "open_in_same_tab": True,
+        },
+        {
+            "title": "Import & export",
+            "url": f"{base_url}/api/import_export.html",
+            "open_in_same_tab": True,
+        },
+    ]
+
+
+@pytest.mark.parametrize("base_url", ["", "/CyteBase"])
+def test_api_pages_keep_the_guide_header_navigation_and_existing_content(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch, base_url: str
+) -> None:
+    pytest.importorskip("jupytext")
+    pytest.importorskip("nbformat")
+    pytest.importorskip("yaml")
+    from docs import build_docs
+
+    monkeypatch.setenv("BASE_URL", base_url)
+    html = tmp_path / "html"
+    api = html / "api"
+    api.mkdir(parents=True)
+    header = (
+        '<nav class="myst-top-nav-bar"><div>'
+        '<button class="myst-top-nav-menu-button flex">Menu</button>'
+        f'<a class="myst-home-link" href="{base_url}/"><img src="logo.svg"/>CyteBase</a>'
+        '</div><button aria-expanded="false" data-state="closed" class="myst-search-bar flex myst-search-bar-disabled">Search'
+        "<script>window.headerScript = true;</script></button>"
+        '<button class="myst-theme-button">Theme</button></nav>'
+    )
+    navigation = (
+        '<nav class="myst-primary-sidebar-toc"><div class="myst-toc">'
+        f'<a class="myst-toc-item myst-toc-item-exact font-bold p-2 my-1" aria-current="page" href="{base_url}/">Overview</a>'
+        f'<a href="{base_url}/tutorials/remote-stores/">Remote stores</a>'
+        f'<a href="{base_url}/api/index.html">API reference</a>'
+        f'<a href="{base_url}/api/cytebase.html">Catalog</a>'
+        "</div></nav>"
+    )
+    (html / "index.html").write_text(
+        f"<html><head></head><body>{header}{navigation}</body></html>"
+    )
+    article = '<article><h1 id="cytebase">Catalog</h1><a href="cytebase.html#method">Method</a></article>'
+    for name in ("index.html", "cytebase.html", "search.html", "genindex.html"):
+        (api / name).write_text(
+            '<html><head></head><body class="docs-api"><header>'
+            '<nav class="docs-header-placeholder"></nav></header>'
+            '<div class="myst-primary-sidebar-nav docs-api-navigation">'
+            '<nav class="docs-api-tree"><ul><li>Original API menu</li></ul></nav>'
+            f"</div>{article}</body></html>"
+        )
+    (api / "objects.inv").write_bytes(b"existing Sphinx inventory")
+    static = api / "_static"
+    static.mkdir()
+    (static / "webpack-macros.html").write_text("{% macro assets() %}{% endmacro %}")
+
+    build_docs.integrate_api_navigation(html)
+
+    for page in api.glob("*.html"):
+        contents = page.read_text()
+        copied_header = build_docs.html_fragment(contents, "myst-top-nav-bar")
+        copied_navigation = build_docs.html_fragment(
+            contents, "myst-primary-sidebar-toc"
+        )
+        assert 'class="myst-search-bar search-button__button"' in copied_header
+        assert (
+            'class="myst-top-nav-menu-button sidebar-toggle primary-toggle"'
+            in copied_header
+        )
+        assert "myst-search-bar-disabled" not in copied_header
+        assert 'aria-label="Search documentation"' in copied_header
+        assert 'aria-controls="pst-search-dialog"' in copied_header
+        assert "aria-expanded" not in copied_header
+        assert "data-state" not in copied_header
+        assert "<script" not in copied_header
+        assert "Original API menu" not in contents
+        assert "font-bold" not in copied_navigation
+        assert "myst-toc-item-exact" not in copied_navigation
+        assert "p-2" not in copied_navigation
+        assert "my-1" not in copied_navigation
+        assert re.findall(r'href="([^"]+)"', copied_navigation) == re.findall(
+            r'href="([^"]+)"', navigation
+        )
+        selected = re.findall(r'<a\b[^>]*aria-current="page"[^>]*>', copied_navigation)
+        if page.name in {"index.html", "cytebase.html"}:
+            assert len(selected) == 1
+            assert f'href="{base_url}/api/{page.name}"' in selected[0]
+        else:
+            assert not selected
+        assert article in contents
+        assert contents.count('src="https://docs.nygen.io/assets/brand/docs.js"') == 1
+        assert "nygen-docs-sidebar:" in contents
+        assert "fonts/inter/latin.woff2" in contents
+    assert (api / "objects.inv").read_bytes() == b"existing Sphinx inventory"
+    assert (
+        static / "webpack-macros.html"
+    ).read_text() == "{% macro assets() %}{% endmacro %}"
+
+
+def test_html_fragment_rejects_missing_or_duplicate_navigation() -> None:
+    pytest.importorskip("jupytext")
+    pytest.importorskip("nbformat")
+    pytest.importorskip("yaml")
+    from docs import build_docs
+
+    for contents in (
+        "<html></html>",
+        '<nav class="menu"></nav><nav class="menu"></nav>',
+    ):
+        with pytest.raises(ValueError, match="Expected one complete .menu element"):
+            build_docs.html_fragment(contents, "menu")
diff --git a/tests/test_docs_structure.py b/tests/test_docs_structure.py
index e93ab1e..6d8ec80 100644
--- a/tests/test_docs_structure.py
+++ b/tests/test_docs_structure.py
@@ -132,6 +132,7 @@ def test_navigation_publishes_every_page() -> None:
         "open_in_same_tab": True,
     } in sections["Reference"]
     assert "llms.txt" in project["static_files"]
+    assert "../build/api" not in project["static_files"]
     assert "reference/api/**" in project["exclude"]
 
     published = _toc_files(toctree)