fix: generate llms.txt from mkdocs nav to fix dead links

.gitignore

@@ -7,6 +7,7 @@ temp*
 .secrets/
 
 # Generated documentation files
+src/llms.txt
 src/llms-full.txt
 site/llms-full.txt
 dj_local_conf.json

docker-compose.yaml

@@ -84,12 +84,13 @@ services:
             # LIVE mode: install datajoint and notebook dependencies for interactive development
             pip install -e /datajoint-python
             pip install scikit-image pooch
+            python scripts/gen_llms_full.py
             mkdocs serve --config-file ./mkdocs.yaml -a 0.0.0.0:8000
         elif echo "$${MODE}" | grep -i build &>/dev/null; then
             # BUILD mode: build static site from pre-executed notebooks
             # Install datajoint-python for mkdocstrings (needs to import for API docs)
             pip install -e /datajoint-python
-            # Generate llms-full.txt with current git info
+            # Generate llms.txt and llms-full.txt
             python scripts/gen_llms_full.py
             mkdocs build --config-file ./mkdocs.yaml
         elif echo "$${MODE}" | grep -i execute_pg &>/dev/null; then

scripts/gen_llms_full.py

@@ -1,22 +1,27 @@
 #!/usr/bin/env python3
 """
-Generate llms-full.txt from documentation sources.
+Generate llms.txt and llms-full.txt from documentation sources.
 
-This script concatenates all markdown documentation into a single file
-optimized for LLM consumption.
+- llms.txt: Index with links derived from mkdocs.yaml nav
+- llms-full.txt: Complete documentation concatenated for LLM consumption
 
-The generated file is NOT committed to git - it's auto-generated during
-the build process with current version metadata.
+Both files are auto-generated during the build process.
 """
 
 import json
+import re
 import subprocess
 from datetime import datetime, timezone
 from pathlib import Path
 
+import yaml
+
 # Documentation root
-DOCS_DIR = Path(__file__).parent.parent / "src"
+PROJECT_DIR = Path(__file__).parent.parent
+DOCS_DIR = PROJECT_DIR / "src"
+MKDOCS_FILE = PROJECT_DIR / "mkdocs.yaml"
 OUTPUT_FILE = DOCS_DIR / "llms-full.txt"
+OUTPUT_INDEX = DOCS_DIR / "llms.txt"
 
 # Sections in order of importance
 SECTIONS = [
@@ -115,6 +120,114 @@ def get_doc_files(directory: Path) -> list[Path]:
     return sorted(files)
 
 
+def source_path_to_url(path: str) -> str:
+    """Convert a source file path to a deployed MkDocs URL.
+
+    MkDocs with use_directory_urls=true (default) serves:
+      about/whats-new-2.md  ->  /about/whats-new-2/
+      tutorials/basics/01-first-pipeline.ipynb  ->  /tutorials/basics/01-first-pipeline/
+      index.md  ->  /
+      section/index.md  ->  /section/
+    """
+    # Strip file extension
+    url = re.sub(r"\.(md|ipynb)$", "", path)
+    # index pages -> parent directory
+    url = re.sub(r"/index$", "", url)
+    if url == "index":
+        return "/"
+    # Avoid double slash for paths like "api/"
+    if url.endswith("/"):
+        return f"/{url}"
+    return f"/{url}/"
+
+
+def extract_nav_entries(nav, section_path=""):
+    """Recursively extract (title, url) pairs from mkdocs nav structure."""
+    entries = []
+    if isinstance(nav, list):
+        for item in nav:
+            entries.extend(extract_nav_entries(item, section_path))
+    elif isinstance(nav, dict):
+        for key, value in nav.items():
+            if isinstance(value, str):
+                # Leaf node: "Title: path.md" or external URL
+                if value.startswith("http"):
+                    continue  # skip external links
+                url = source_path_to_url(value)
+                entries.append((key, url))
+            elif isinstance(value, list):
+                # Section with children
+                entries.extend(extract_nav_entries(value, key))
+    elif isinstance(nav, str):
+        # Bare path without title (e.g., index pages)
+        if not nav.startswith("http"):
+            url = source_path_to_url(nav)
+            entries.append((None, url))
+    return entries
+
+
+def load_mkdocs_nav():
+    """Load just the nav section from mkdocs.yaml.
+
+    mkdocs.yaml contains !!python/name tags that standard YAML loaders
+    can't resolve without the material theme installed. We add a custom
+    constructor that ignores these tags.
+    """
+    loader = yaml.SafeLoader
+    # Handle !!python/name and !!python/object tags by returning None
+    loader.add_multi_constructor(
+        "tag:yaml.org,2002:python/",
+        lambda loader, suffix, node: None,
+    )
+    with open(MKDOCS_FILE, "r") as f:
+        return yaml.load(f, Loader=loader)
+
+
+def generate_llms_txt():
+    """Generate llms.txt index from mkdocs.yaml nav."""
+    mkdocs_config = load_mkdocs_nav()
+
+    nav = mkdocs_config.get("nav", [])
+
+    # Map top-level nav sections to llms.txt sections
+    # Each top-level nav item is a dict like {"Concepts": [...]}
+    lines = [
+        "# DataJoint Documentation",
+        "",
+        "> DataJoint is a Python framework for building scientific data pipelines "
+        "with automated computation, integrity constraints, and seamless integration "
+        "of relational databases with object storage.",
+        "",
+        "> For the complete documentation in a single file, see [/llms-full.txt](/llms-full.txt)",
+        "",
+    ]
+
+    for nav_item in nav:
+        if isinstance(nav_item, dict):
+            for section_name, section_content in nav_item.items():
+                if isinstance(section_content, str):
+                    # Skip "Home: index.md" but keep other top-level leaves
+                    if section_content == "index.md" or section_content.startswith("http"):
+                        continue
+                    url = source_path_to_url(section_content)
+                    lines.append(f"- [{section_name}]({url})")
+                    lines.append("")
+                elif isinstance(section_content, list):
+                    lines.append(f"## {section_name}")
+                    lines.append("")
+                    entries = extract_nav_entries(section_content)
+                    for title, url in entries:
+                        if title:
+                            lines.append(f"- [{title}]({url})")
+                    lines.append("")
+
+    content = "\n".join(lines) + "\n"
+    with open(OUTPUT_INDEX, "w", encoding="utf-8") as f:
+        f.write(content)
+
+    print(f"Generated {OUTPUT_INDEX} ({len(content):,} bytes)")
+
+
 def generate_llms_full():
     """Generate the llms-full.txt file."""
     # Get current git info for version metadata
@@ -153,4 +266,5 @@ def generate_llms_full():
 
 
 if __name__ == "__main__":
+    generate_llms_txt()
     generate_llms_full()