Support source file suffix detection (#21)

* Move readme content to index.rst

* Clean up project name

* Add advanced configuration

.readthedocs.yml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

CHANGELOG.rst

@@ -1,6 +1,22 @@
 Changelog
 =========
 
+0.2.4
+-----
+
+- Support source file suffix detection
+  `#21 <https://github.com/jdillard/sphinx-llms-txt/pull/21>`_
+
+0.2.3
+-----
+
+- Remove ``get_and_resolve_toctree`` method
+  `#19 <https://github.com/jdillard/sphinx-llms-txt/pull/19>`_
+- Simplify ``_sources`` lookup
+  `#18 <https://github.com/jdillard/sphinx-llms-txt/pull/18>`_
+- Add sphinx docs
+  `#16 <https://github.com/jdillard/sphinx-llms-txt/pull/16>`_
+
 0.2.2
 -----
 

README.md

@@ -1,91 +1,14 @@
 # Sphinx llms.txt generator
 
-A Sphinx extension that generates a summary `llms.txt` file, written in Markdown, and a single combined documentation `llms-full.txt` file, written in reStructuredText.
+A Sphinx extension that generates a summary `llms.txt` file and a single combined documentation `llms-full.txt` file.
 
 [![PyPI version](https://img.shields.io/pypi/v/sphinx-llms-txt.svg)](https://pypi.python.org/pypi/sphinx-llms-txt)
 [![Downloads](https://static.pepy.tech/badge/sphinx-llms-txt/month)](https://pepy.tech/project/sphinx-llms-txt)
+[![Parallel Safe](https://img.shields.io/badge/parallel%20safe-true-brightgreen)](#)
 
-## Installation
+## Documentation
 
-```bash
-pip install sphinx-llms-txt
-```
-
-## Usage
-
-1. Add the extension to your Sphinx configuration (`conf.py`):
-
-```python
-extensions = [
-    'sphinx_llms_txt',
-]
-```
-
-## Configuration Options
-
-### `llms_txt_full_file`
-
-- **Type**: boolean
-- **Default**: `'True'`
-- **Description**: Whether to write the single output file
-
-### `llms_txt_full_filename`
-
-- **Type**: string
-- **Default**: `'llms-full.txt'`
-- **Description**: Name of the single output file
-
-### `llms_txt_full_max_size`
-
-- **Type**: integer or `None`
-- **Default**: `None` (no limit)
-- **Description**: Sets a maximum line count for `llms_txt_full_filename`.
-  If exceeded, the file is skipped and a warning is shown, but the build still completes.
-
-### `llms_txt_file`
-
-- **Type**: boolean
-- **Default**: `True`
-- **Description**: Whether to write the summary information file
-
-### `llms_txt_filename`
-
-- **Type**: string
-- **Default**: `llms.txt`
-- **Description**: Name of the summary information file
-
-### `llms_txt_directives`
-
-- **Type**: list of strings
-- **Default**: `[]`
-- **Description**: List of custom directive names to process for path resolution.
-
-### `llms_txt_title`
-
-- **Type**: string or `None`
-- **Default**: `None`
-- **Description**: Overrides the Sphinx project name as the heading in `llms.txt`.
-
-### `llms_txt_summary`
-
-- **Type**: string or `None`
-- **Default**: `None`
-- **Description**: Optional, but recommended, summary description for `llms.txt`.
-
-### `llms_txt_exclude`
-
-- **Type**: list of strings
-- **Default**: `[]`
-- **Description**: A list of pages to ignore  (e.g., `["page1", "page_with_*"]`).
-
-## Features
-
-- Creates `llms.txt` and `llms-full.txt`
-- Automatically add content from `include` directives
-- Resolves relative paths in directives like `image` and `figure` to use full paths
-  - Ability to add list of custom directives with `llms_txt_directives`
-  - Optionally, prepend a base URL using Sphinx's `html_baseurl`
-- Ability to exclude pages
+See [sphinx-llms-txt documentation](https://sphinx-llms-txt.readthedocs.io/en/latest/index.html) for installation and configuration instructions.
 
 ## License
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = SphinxLLMsTxt
+SOURCEDIR     = source
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

@@ -0,0 +1,6 @@
+furo
+esbonio
+sphinx-contributors
+sphinx
+sphinx-llms-txt
+sphinxext-opengraph

docs/source/advanced-configuration.rst

@@ -0,0 +1,170 @@
+Advanced Configuration
+======================
+
+This page covers advanced configuration options for the sphinx-llms-txt extension.
+
+.. _customizing_llms_files:
+
+Customizing the LLMs Files
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+By default, the extension generates two files:
+
+1. ``llms.txt`` - A summary file in Markdown format
+2. ``llms-full.txt`` - A complete documentation file in reStructuredText format
+
+You can customize these files in several ways:
+
+.. _changing_filenames:
+
+Changing Filenames
+~~~~~~~~~~~~~~~~~~
+
+You can change the default filenames by setting these values in your ``conf.py``:
+
+.. code-block:: python
+
+   llms_txt_filename = "custom-summary.txt"
+   llms_txt_full_filename = "custom-docs.txt"
+
+.. _disabling_file_generation:
+
+Disabling File Generation
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you only want one of the files, you can disable generation of the other:
+
+.. code-block:: python
+
+   # Disable summary file
+   llms_txt_file = False
+
+   # Disable full documentation file
+   llms_txt_full_file = False
+
+.. _custom_summary:
+
+Adding a Custom Summary
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The summary file can include a custom description of your project:
+
+.. code-block:: python
+
+   llms_txt_summary = """
+   This documentation explains how to use MyProject to build amazing
+   applications. The project provides a comprehensive API for handling
+   data processing and visualization.
+   """
+
+.. note:: The summary can span multiple lines and will be properly formatted in the output file.
+
+.. _custom_title:
+
+Custom Title
+~~~~~~~~~~~~
+
+By default, the project name from Sphinx is used as the title in ``llms.txt``. You can override this:
+
+.. code-block:: python
+
+   llms_txt_title = "My Custom Project Documentation"
+
+.. _handling_large_documentation:
+
+Handling Large Documentation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For very large documentation sets, generating the full documentation file might exceed reasonable size limits.
+You can set a maximum line count:
+
+.. code-block:: python
+
+   llms_txt_full_max_size = 10000  # Maximum 10,000 lines
+
+If the generated file would exceed this limit, the extension will skip its generation and show a warning, allowing the build to complete.
+
+.. tip:: Use :ref:`excluding_content` to remove less relevant pages.
+
+.. _custom_directive_handling:
+
+Custom Directive Handling
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. _path_resolution:
+
+Path Resolution
+~~~~~~~~~~~~~~~
+
+The extension resolves paths in the common directives ``[ 'image', 'figure']`` by default.
+You can add custom directives to this list:
+
+.. code-block:: python
+
+   llms_txt_directives = [
+       "my-custom-image-directive",
+       "another-directive-with-paths",
+   ]
+
+This ensures that paths in your custom directives are properly resolved in the generated files.
+
+.. _excluding_content:
+
+Excluding Content
+^^^^^^^^^^^^^^^^^
+
+You can exclude specific pages from being included in the generated files:
+
+.. code-block:: python
+
+   llms_txt_exclude = [
+       "search",  # Exclude the search page
+       "genindex",  # Exclude the index page
+       "private_*",  # Exclude all pages starting with 'private_'
+   ]
+
+This is useful for excluding auto-generated pages, indexes, or content that isn't relevant for LLM consumption.
+
+.. _using_html_baseurl:
+
+Using HTML Base URL
+^^^^^^^^^^^^^^^^^^^
+
+If you want to include absolute URLs for resources in your documentation, you can use Sphinx's built-in ``html_baseurl`` configuration:
+
+.. code-block:: python
+
+   html_baseurl = "https://example.com/docs/"
+
+When this option is set, all resolved paths in directives will be prefixed with this URL, creating absolute paths in the generated files.
+
+.. _integration_examples:
+
+Integration Examples
+^^^^^^^^^^^^^^^^^^^^
+
+Complete Configuration Example
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Here's a complete example showing multiple :ref:`configuration-values`:
+
+.. code-block:: python
+
+   # File names and generation options
+   llms_txt_filename = "ai-summary.txt"
+   llms_txt_full_filename = "ai-full-docs.txt"
+   llms_txt_full_max_size = 50000
+
+   # Content customization
+   llms_txt_title = "Project Documentation for AI Assistants"
+   llms_txt_summary = """
+   This is a comprehensive documentation set for our project.
+   It includes API references, usage examples, and tutorials.
+   """
+
+   # Path handling
+   html_baseurl = "https://docs.example.com/"
+   llms_txt_directives = ["custom-image", "custom-include"]
+
+   # Content filtering
+   llms_txt_exclude = ["search", "genindex", "404", "private_*"]

docs/source/changelog.rst

@@ -0,0 +1 @@
+.. include:: ../../CHANGELOG.rst

docs/source/conf.py

@@ -0,0 +1,101 @@
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+import re
+import subprocess
+
+# -- Project information -----------------------------------------------------
+
+project = "sphinx-llms-txt"
+copyright = "Jared Dillard"
+author = "Jared Dillard"
+llms_txt_summary = """
+A Sphinx extension that generates a summary llms.txt file,written in Markdown,
+and a single combined documentation llms-full.txt file, written in reStructuredText.
+"""
+
+# check if the current commit is tagged as a release (vX.Y.Z)
+try:
+    GIT_TAG_OUTPUT = subprocess.check_output(["git", "tag", "--points-at", "HEAD"])
+    current_tag = GIT_TAG_OUTPUT.decode().strip()
+    if re.match(r"^v(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)$", current_tag):
+        version = current_tag
+    else:
+        version = "latest"
+except (subprocess.CalledProcessError, FileNotFoundError):
+    version = "latest"
+
+# The full version, including alpha/beta/rc tags
+release = ""
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.intersphinx",
+    "sphinx_contributors",
+    "sphinx_llms_txt",
+]
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+intersphinx_mapping = {
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {}
+
+html_baseurl = "https://sphinx-llms-txt.readthedocs.org/"
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "SphinxLLMsTxtdoc"
+
+
+def setup(app):
+    app.add_object_type(
+        "confval",
+        "confval",
+        objname="configuration value",
+        indextemplate="pair: %s; configuration value",
+    )

docs/source/configuration-values.rst

@@ -0,0 +1,84 @@
+Project Configuration Values
+============================
+
+.. confval:: llms_txt_full_file
+
+   - **Type**: boolean
+   - **Default**: ``True``
+   - **Description**: Whether to write the single output file.
+     See :ref:`disabling_file_generation`.
+
+   .. versionadded:: 0.1.0
+
+.. confval:: llms_txt_full_filename
+
+   - **Type**: string
+   - **Default**: ``'llms-full.txt'``
+   - **Description**: Name of the single output file.
+     See :ref:`changing_filenames`.
+
+   .. versionadded:: 0.1.0
+
+.. confval:: llms_txt_full_max_size
+
+   - **Type**: integer or ``None``
+   - **Default**: ``None`` (no limit)
+   - **Description**: Sets a maximum line count for ``llms_txt_full_filename``.
+     If exceeded, the file is skipped and a warning is shown, but the build still completes.
+     See :ref:`handling_large_documentation`.
+
+   .. versionadded:: 0.2.0
+
+.. confval:: llms_txt_file
+
+   - **Type**: boolean
+   - **Default**: ``True``
+   - **Description**: Whether to write the summary information file.
+     See :ref:`disabling_file_generation`.
+
+   .. versionadded:: 0.2.0
+
+.. confval:: llms_txt_filename
+
+   - **Type**: string
+   - **Default**: ``llms.txt``
+   - **Description**: Name of the summary information file.
+     See :ref:`changing_filenames`.
+
+   .. versionadded:: 0.2.0
+
+.. confval:: llms_txt_directives
+
+   - **Type**: list of strings
+   - **Default**: ``[]`` (empty list)
+   - **Description**: List of custom directive names to process for path resolution.
+     See :ref:`path_resolution`.
+
+   .. versionadded:: 0.1.0
+
+.. confval:: llms_txt_title
+
+   - **Type**: string or ``None``
+   - **Default**: ``None``
+   - **Description**: Overrides the Sphinx project name as the heading in ``llms.txt``.
+     See :ref:`custom_title`.
+
+   .. versionadded:: 0.2.0
+
+.. confval:: llms_txt_summary
+
+   - **Type**: string or ``None``
+   - **Default**: ``None``
+   - **Description**: Optional, but recommended, summary description for ``llms.txt``.
+     See :ref:`custom_summary`.
+
+   .. versionadded:: 0.2.0
+
+.. confval:: llms_txt_exclude
+
+   - **Type**: list of strings
+   - **Default**: ``[]``
+   - **Description**: A list of pages to ignore.
+     See :ref:`excluding_content`.
+
+   .. versionadded:: 0.2.1

docs/source/contributing.rst

@@ -0,0 +1,48 @@
+Contributing
+============
+
+You will need to set up a development environment to make and test your changes before submitting them.
+
+Local development
+-----------------
+
+#. Clone the `sphinx-llms-txt repository`_.
+
+#. Create and activate a virtual environment:
+
+   .. code-block:: console
+
+      python3 -m venv .venv
+      source .venv/bin/activate
+
+#. Install development dependencies:
+
+   .. code-block:: console
+
+      pip install -e ".[dev]"
+
+#. Install pre-commit Git hook scripts:
+
+   .. code-block:: console
+
+      pre-commit install
+
+Testing changes
+---------------
+
+Run ``pytest`` before committing changes.
+
+Current contributors
+--------------------
+
+Thanks to all who have contributed!
+The people that have improved the code:
+
+.. contributors:: jdillard/sphinx-llms-txt
+   :avatars:
+   :limit: 100
+   :exclude: pre-commit-ci[bot],dependabot[bot]
+   :order: ASC
+
+
+.. _sphinx-llms-txt repository: https://github.com/jdillard/sphinx-llms-txt

docs/source/getting-started.rst

@@ -0,0 +1,50 @@
+Getting Started
+===============
+
+Demo
+----
+
+You can see this Sphinx project's `llms.txt`_ and `llms-full.txt`_ files as a simple example.
+
+Installation
+------------
+
+Directly install via ``pip`` by using:
+
+.. code-block:: bash
+
+    pip install sphinx-llms-txt
+
+Usage
+-----
+
+Add the extension to your Sphinx configuration (``conf.py``):
+
+.. code-block:: python
+
+    extensions = [
+        'sphinx_llms_txt',
+    ]
+
+Once added, the extension will automatically generate the LLMs.txt files during the build process.
+
+See :doc:`advanced-configuration` for more information about how to use **sphinx-llms-txt**.
+
+How It Works
+-----------
+
+During the Sphinx build process:
+
+1. **Content Collection**: Scans all of your documentation's ``_source`` pages and collects their content
+2. **Directive Processing**: Resolves ``include`` directives by automatically incorporating their content
+3. **Path Resolution**: Transforms relative paths in directives to full paths
+4. **Output Generation**: Creates two optional files:
+
+   - ``llms.txt``: A concise summary of your documentation, in Markdown
+   - ``llms-full.txt``: A comprehensive version with all documentation content, in reStructuredText
+
+5. **Content Filtering**: Allows you to exclude specific pages from the generated files
+
+
+.. _llms.txt: https://sphinx-llms-txt.readthedocs.io/en/latest/llms.txt
+.. _llms-full.txt: https://sphinx-llms-txt.readthedocs.io/en/latest/llms-full.txt

docs/source/index.rst

@@ -0,0 +1,31 @@
+Sphinx llms.txt Generator
+=========================
+
+A `Sphinx`_ extension that generates a summary ``llms.txt`` file, written in Markdown, and a single combined documentation ``llms-full.txt`` file, written in reStructuredText.
+
+|PyPI version| |Downloads| |Parallel Safe| |GitHub Stars|
+
+.. toctree::
+   :maxdepth: 2
+
+   getting-started
+   advanced-configuration
+   configuration-values
+   contributing
+   changelog
+
+
+.. _Sphinx: http://sphinx-doc.org/
+
+.. |PyPI version| image:: https://img.shields.io/pypi/v/sphinx-llms-txt.svg
+   :target: https://pypi.python.org/pypi/sphinx-llms-txt
+   :alt: Latest PyPi Version
+.. |Downloads| image:: https://static.pepy.tech/badge/sphinx-llms-txt/month
+    :target: https://pepy.tech/project/sphinx-llms-txt
+    :alt: PyPi Downloads per month
+.. |Parallel Safe| image:: https://img.shields.io/badge/parallel%20safe-true-brightgreen
+   :target: #
+   :alt: Parallel read/write safe
+.. |GitHub Stars| image:: https://img.shields.io/github/stars/jdillard/sphinx-llms-txt?style=social
+   :target: https://github.com/jdillard/sphinx-llms-txt
+   :alt: GitHub Repository stars

sphinx_llms_txt/__init__.py

@@ -12,7 +12,7 @@ from .manager import LLMSFullManager
 from .processor import DocumentProcessor
 from .writer import FileWriter
 
-__version__ = "0.2.2"
+__version__ = "0.2.4"
 
 # Export classes needed by tests
 __all__ = [

sphinx_llms_txt/collector.py

@@ -3,7 +3,7 @@ Document collector module for sphinx-llms-txt.
 """
 
 import fnmatch
-from typing import Any, Dict, List
+from typing import Any, Dict, List, Tuple
 
 from sphinx.environment import BuildEnvironment
 from sphinx.util import logging
@@ -19,6 +19,7 @@ class DocumentCollector:
         self.master_doc: str = None
         self.env: BuildEnvironment = None
         self.config: Dict[str, Any] = {}
+        self.app = None
 
     def set_master_doc(self, master_doc: str):
         """Set the master document name."""
@@ -37,8 +38,73 @@ class DocumentCollector:
         """Set configuration options."""
         self.config = config
 
-    def get_page_order(self) -> List[str]:
-        """Get the correct page order from the toctree structure."""
+    def set_app(self, app):
+        """Set the Sphinx application reference."""
+        self.app = app
+
+    def _get_source_suffixes(self):
+        """Get all valid source file suffixes from Sphinx configuration.
+
+        Returns:
+            list: List of source file suffixes (e.g., ['.rst', '.md', '.txt'])
+        """
+        if not self.app:
+            return [".rst"]  # Default fallback
+
+        source_suffix = self.app.config.source_suffix
+
+        if isinstance(source_suffix, dict):
+            return list(source_suffix.keys())
+        elif isinstance(source_suffix, list):
+            return source_suffix
+        else:
+            return [source_suffix]  # String format
+
+    def _get_docname_suffix(self, docname: str, sources_dir) -> str:
+        """
+        Determine the source suffix for a given docname by checking which
+        file exists.
+
+        Args:
+            docname: The document name to check
+            sources_dir: Path to the _sources directory
+
+        Returns:
+            The source suffix if found, or None if no matching file exists
+        """
+        if not sources_dir or not sources_dir.exists():
+            return None
+
+        # Get the source link suffix from Sphinx config
+        source_link_suffix = ""
+        if self.app and hasattr(self.app.config, "html_sourcelink_suffix"):
+            source_link_suffix = self.app.config.html_sourcelink_suffix
+            # Handle empty string case specially
+            if source_link_suffix == "":
+                source_link_suffix = ""  # Keep it empty
+            elif not source_link_suffix.startswith("."):
+                source_link_suffix = "." + source_link_suffix
+
+        # Get the source file suffixes from Sphinx config
+        source_suffixes = self._get_source_suffixes()
+
+        # Try to find the source file with any of the valid source suffixes
+        for src_suffix in source_suffixes:
+            candidate_file = sources_dir / f"{docname}{src_suffix}{source_link_suffix}"
+            if candidate_file.exists():
+                return src_suffix
+
+        return None
+
+    def get_page_order(self, sources_dir=None) -> List[Tuple[str, str]]:
+        """Get the correct page order from the toctree structure.
+
+        Args:
+            sources_dir: Optional path to _sources directory for suffix detection
+
+        Returns:
+            List of tuples (docname, source_suffix) in toctree order
+        """
         if not self.env or not self.master_doc:
             return []
 
@@ -52,9 +118,12 @@ class DocumentCollector:
 
             visited.add(docname)
 
-            # Add the current document
-            if docname not in page_order:
-                page_order.append(docname)
+            # Add the current document with its suffix
+            if docname not in [doc for doc, _ in page_order]:
+                suffix = None
+                if sources_dir:
+                    suffix = self._get_docname_suffix(docname, sources_dir)
+                page_order.append((docname, suffix))
 
             # Check for toctree entries in this document
             try:
@@ -65,21 +134,34 @@ class DocumentCollector:
                 ):
                     for child_docname in self.env.toctree_includes[docname]:
                         collect_from_toctree(child_docname)
-                else:
-                    # Fallback: try to resolve and parse the toctree
-                    toctree = self.env.get_and_resolve_toctree(docname, None)
-                    if toctree:
-                        from docutils import nodes
+                # Try to use dependencies to find related documents
+                elif (
+                    hasattr(self.env, "dependencies")
+                    and docname in self.env.dependencies
+                ):
+                    # Extract the dependent documents from the dependencies dict
+                    for child_docname in self.env.dependencies[docname]:
+                        # Only add documents actually in the document set
+                        if (
+                            hasattr(self.env, "all_docs")
+                            and child_docname in self.env.all_docs
+                        ):
+                            collect_from_toctree(child_docname)
+                # Fallback to titles or other available references
+                elif hasattr(self.env, "titles") and hasattr(self.env, "all_docs"):
+                    # Get all document names
+                    all_docnames = list(self.env.all_docs.keys())
 
-                        for node in list(toctree.findall(nodes.reference)):
-                            if "refuri" in node.attributes:
-                                refuri = node.attributes["refuri"]
-                                if refuri and refuri.endswith(".html"):
-                                    child_docname = refuri[:-5]  # Remove .html
-                                    if (
-                                        child_docname != docname
-                                    ):  # Avoid circular references
-                                        collect_from_toctree(child_docname)
+                    # Look for documents that might be related (have similar paths)
+                    current_prefix = "/".join(docname.split("/")[:-1])
+                    if current_prefix:
+                        for child_docname in all_docnames:
+                            # Documents in the same directory might be related
+                            if (
+                                child_docname.startswith(current_prefix)
+                                and child_docname != docname
+                            ):
+                                collect_from_toctree(child_docname)
             except Exception as e:
                 logger.debug(f"Could not get toctree for {docname}: {e}")
 
@@ -88,22 +170,33 @@ class DocumentCollector:
 
         # Add any remaining documents not in the toctree (sorted)
         if hasattr(self.env, "all_docs"):
+            processed_docnames = {doc for doc, _ in page_order}
             remaining = sorted(
-                [doc for doc in self.env.all_docs.keys() if doc not in page_order]
+                [
+                    doc
+                    for doc in self.env.all_docs.keys()
+                    if doc not in processed_docnames
+                ]
             )
-            page_order.extend(remaining)
+            for docname in remaining:
+                suffix = None
+                if sources_dir:
+                    suffix = self._get_docname_suffix(docname, sources_dir)
+                page_order.append((docname, suffix))
 
         return page_order
 
-    def filter_excluded_pages(self, page_order: List[str]) -> List[str]:
+    def filter_excluded_pages(
+        self, page_order: List[Tuple[str, str]]
+    ) -> List[Tuple[str, str]]:
         """Filter out excluded pages from the page order."""
         exclude_patterns = self.config.get("llms_txt_exclude")
         if exclude_patterns:
             return [
-                page
-                for page in page_order
+                (docname, suffix)
+                for docname, suffix in page_order
                 if not any(
-                    self._match_exclude_pattern(page, pattern)
+                    self._match_exclude_pattern(docname, pattern)
                     for pattern in exclude_patterns
                 )
             ]

sphinx_llms_txt/manager.py

@@ -56,6 +56,7 @@ class LLMSFullManager:
     def set_app(self, app: Sphinx):
         """Set the Sphinx application reference."""
         self.app = app
+        self.collector.set_app(app)
         if self.writer:
             self.writer.app = app
 
@@ -69,23 +70,7 @@ class LLMSFullManager:
         self.processor = DocumentProcessor(self.config, srcdir)
         self.writer = FileWriter(self.config, outdir, self.app)
 
-        # Get the correct page order
-        page_order = self.collector.get_page_order()
-
-        if not page_order:
-            logger.warning(
-                "Could not determine page order, skipping llms-full creation"
-            )
-            return
-
-        # Apply exclusion filter if configured
-        page_order = self.collector.filter_excluded_pages(page_order)
-
-        # Determine output file name and location
-        output_filename = self.config.get("llms_txt_full_filename")
-        output_path = Path(outdir) / output_filename
-
-        # Find sources directory
+        # Find sources directory first so we can pass it to get_page_order
         sources_dir = None
         possible_sources = [
             Path(outdir) / "_sources",
@@ -104,14 +89,23 @@ class LLMSFullManager:
             )
             return
 
-        # Collect all available source files
-        txt_files = {}
-        for f in sources_dir.glob("**/*.txt"):
-            logger.debug(f"sphinx-llms-txt: Found source file: {f.stem} at {f}")
-            txt_files[f.stem] = f
+        # Get the correct page order with source suffixes
+        page_order = self.collector.get_page_order(sources_dir)
+
+        if not page_order:
+            logger.warning(
+                "Could not determine page order, skipping llms-full creation"
+            )
+            return
+
+        # Apply exclusion filter if configured
+        page_order = self.collector.filter_excluded_pages(page_order)
+
+        # Determine output file name and location
+        output_filename = self.config.get("llms_txt_full_filename")
+        output_path = Path(outdir) / output_filename
 
         # Log discovered files and page order
-        logger.debug(f"sphinx-llms-txt: Found {len(txt_files)} source files")
         logger.debug(f"sphinx-llms-txt: Page order (after exclusion): {page_order}")
 
         # Log exclusion patterns
@@ -119,33 +113,43 @@ class LLMSFullManager:
         if exclude_patterns:
             logger.debug(f"sphinx-llms-txt: Exclusion patterns: {exclude_patterns}")
 
-        # Create a mapping from docnames to actual file names
+        # Create a mapping from docnames to source files
         docname_to_file = {}
 
-        # Try exact matches first
-        for docname in page_order:
+        # Get the source link suffix from Sphinx config
+        source_link_suffix = (
+            self.app.config.html_sourcelink_suffix if self.app else ".txt"
+        )
+
+        # Handle empty string case specially
+        if source_link_suffix == "":
+            source_link_suffix = ""  # Keep it empty
+        elif not source_link_suffix.startswith("."):
+            source_link_suffix = "." + source_link_suffix
+
+        # Process each (docname, suffix) in the page order
+        for docname, src_suffix in page_order:
             # Skip excluded pages
-            if any(
+            if exclude_patterns and any(
                 self.collector._match_exclude_pattern(docname, pattern)
                 for pattern in exclude_patterns
             ):
                 continue
 
-            if docname in txt_files:
-                docname_to_file[docname] = txt_files[docname]
+            # Build the source file path directly using the known suffix
+            if src_suffix:
+                source_file = sources_dir / f"{docname}{src_suffix}{source_link_suffix}"
+                if source_file.exists():
+                    docname_to_file[docname] = source_file
+                else:
+                    logger.warning(
+                        f"sphinx-llms-txt: Source file not found for: {docname}."
+                        f"Expected: {docname}{src_suffix}{source_link_suffix}"
+                    )
             else:
-                # Try with .rst extension
-                if f"{docname}.rst" in txt_files:
-                    docname_to_file[docname] = txt_files[f"{docname}.rst"]
-                # Try with .txt extension
-                elif f"{docname}.txt" in txt_files:
-                    docname_to_file[docname] = txt_files[f"{docname}.txt"]
-                # Try with underscores instead of hyphens
-                elif docname.replace("-", "_") in txt_files:
-                    docname_to_file[docname] = txt_files[docname.replace("-", "_")]
-                # Try with hyphens instead of underscores
-                elif docname.replace("_", "-") in txt_files:
-                    docname_to_file[docname] = txt_files[docname.replace("_", "-")]
+                logger.warning(
+                    f"sphinx-llms-txt: No source suffix determined for: {docname}"
+                )
 
         # Generate content
         content_parts = []
@@ -156,7 +160,7 @@ class LLMSFullManager:
         max_lines = self.config.get("llms_txt_full_max_size")
         abort_due_to_max_lines = False
 
-        for docname in page_order:
+        for docname, _ in page_order:
             if docname in docname_to_file:
                 file_path = docname_to_file[docname]
                 content, line_count = self._read_source_file(file_path, docname)
@@ -190,65 +194,68 @@ class LLMSFullManager:
                     added_files.add(file_path.stem)
                     total_line_count += line_count
             else:
-                logger.warning(f"sphinx-llm-txt: Source file not found for: {docname}")
+                logger.warning(
+                    f"sphinx-llms-txt: Source file not found for: {docname}. Check that"
+                    f" file exists at _sources/{docname}[suffix]{source_link_suffix}"
+                )
 
-        # Add any remaining files (in alphabetical order) if not aborted
+        # Add any remaining files (in alphabetical order) that aren't in the page order
         if not abort_due_to_max_lines:
-            # Apply the same exclusion filter to remaining files
-            exclude_patterns = self.config.get("llms_txt_exclude")
+            # Get all source files in the _sources directory using configured suffixes
+            source_suffixes = self._get_source_suffixes()
+            all_source_files = []
+            for src_suffix in source_suffixes:
+                glob_pattern = f"**/*{src_suffix}{source_link_suffix}"
+                all_source_files.extend(sources_dir.glob(glob_pattern))
 
-            # Create a set of files to exclude based on their basename
-            excluded_files = set()
-            for pattern in exclude_patterns:
-                if "*" not in pattern and "?" not in pattern:
-                    # For exact patterns, add variants
-                    excluded_files.add(pattern)
-                    excluded_files.add(f"{pattern}.rst")
-                    excluded_files.add(f"{pattern}.txt")
-                    excluded_files.add(pattern.replace("-", "_"))
-                    excluded_files.add(pattern.replace("_", "-"))
+            processed_paths = set(file.resolve() for file in docname_to_file.values())
 
-            # Filter remaining files
-            remaining_files = sorted(
-                [
-                    name
-                    for name in txt_files
-                    if name not in added_files
-                    and name not in excluded_files
-                    and not any(
-                        self.collector._match_exclude_pattern(name, pattern)
-                        for pattern in exclude_patterns
-                    )
-                ]
-            )
-            if remaining_files:
-                logger.info(f"Adding remaining files: {remaining_files}")
-            for file_stem in remaining_files:
-                file_path = txt_files[file_stem]
-                content, line_count = self._read_source_file(file_path, file_stem)
+            # Find files that haven't been processed yet
+            remaining_source_files = [
+                f for f in all_source_files if f.resolve() not in processed_paths
+            ]
+
+            # Sort the remaining files for consistent ordering
+            remaining_source_files.sort()
+
+            if remaining_source_files:
+                logger.info(
+                    f"Found {len(remaining_source_files)} additional files not in"
+                    f" toctree"
+                )
+
+            for file_path in remaining_source_files:
+                # Extract docname from path by removing the source and link suffixes
+                rel_path = str(file_path.relative_to(sources_dir))
+                docname = None
+
+                # Try each source suffix to find which one this file uses
+                for src_suffix in source_suffixes:
+                    combined_suffix = f"{src_suffix}{source_link_suffix}"
+                    if rel_path.endswith(combined_suffix):
+                        docname = rel_path[: -len(combined_suffix)]  # Remove suffix
+                        break
+
+                if docname is None:
+                    continue
+
+                # Skip excluded docnames
+                if exclude_patterns and any(
+                    self.collector._match_exclude_pattern(docname, pattern)
+                    for pattern in exclude_patterns
+                ):
+                    logger.debug(f"sphinx-llms-txt: Skipping excluded file: {docname}")
+                    continue
+
+                # Read and process the file
+                content, line_count = self._read_source_file(file_path, docname)
 
                 # Check if adding this file would exceed the maximum line count
                 if max_lines is not None and total_line_count + line_count > max_lines:
                     break
 
-                # Double-check that this file should be included
-                should_include = True
-                file_stem = file_path.stem
-                exclude_patterns = self.config.get("llms_txt_exclude")
-
-                if exclude_patterns:
-                    # Check stem against exclusion patterns
-                    if any(
-                        self.collector._match_exclude_pattern(file_stem, pattern)
-                        for pattern in exclude_patterns
-                    ):
-                        logger.debug(
-                            "sphinx-llms-txt: Final exclusion check removed remaining"
-                            f" file: {file_stem}"
-                        )
-                        should_include = False
-
-                if content and should_include:
+                if content:
+                    logger.debug(f"sphinx-llms-txt: Adding remaining file: {docname}")
                     content_parts.append(content)
                     total_line_count += line_count
 
@@ -258,7 +265,7 @@ class LLMSFullManager:
             max_lines is not None and total_line_count > max_lines
         ):
             logger.warning(
-                f"sphinx-llm-txt: Max line limit ({max_lines}) exceeded:"
+                f"sphinx-llms-txt: Max line limit ({max_lines}) exceeded:"
                 f" {total_line_count} > {max_lines}. "
                 f"Not creating llms-full.txt file."
             )
@@ -325,5 +332,23 @@ class LLMSFullManager:
             return content_str, line_count + 1
 
         except Exception as e:
-            logger.error(f"sphinx-llm-txt: Error reading source file {file_path}: {e}")
+            logger.error(f"sphinx-llms-txt: Error reading source file {file_path}: {e}")
             return "", 0
+
+    def _get_source_suffixes(self):
+        """Get all valid source file suffixes from Sphinx configuration.
+
+        Returns:
+            list: List of source file suffixes (e.g., ['.rst', '.md', '.txt'])
+        """
+        if not self.app:
+            return [".rst"]  # Default fallback
+
+        source_suffix = self.app.config.source_suffix
+
+        if isinstance(source_suffix, dict):
+            return list(source_suffix.keys())
+        elif isinstance(source_suffix, list):
+            return source_suffix
+        else:
+            return [source_suffix]  # String format

sphinx_llms_txt/writer.py

@@ -3,7 +3,7 @@ File writer module for sphinx-llms-txt.
 """
 
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any, Dict, List, Tuple, Union
 
 from sphinx.application import Sphinx
 from sphinx.util import logging
@@ -42,19 +42,19 @@ class FileWriter:
             )
             return True
         except Exception as e:
-            logger.error(f"sphinx-llm-txt: Error writing combined sources file: {e}")
+            logger.error(f"sphinx-llms-txt: Error writing combined sources file: {e}")
             return False
 
     def write_verbose_info_to_file(
         self,
-        page_order: List[str],
+        page_order: Union[List[str], List[Tuple[str, str]]],
         page_titles: Dict[str, str],
         total_line_count: int = 0,
     ) -> bool:
         """Write summary information to the llms.txt file.
 
         Args:
-            page_order: Ordered list of document names
+            page_order: Ordered list of document names or (docname, suffix) tuples
             page_titles: Dictionary mapping docnames to titles
             total_line_count: Total number of lines in the combined content
 
@@ -86,6 +86,11 @@ class FileWriter:
                 # Add description if available
                 description = self.config.get("llms_txt_summary", "")
                 if description:
+                    # Trim leading and trailing whitespace
+                    description = description.strip()
+                    # Replace newlines with newline + blockquote marker to maintain
+                    # blockquote formatting
+                    description = description.replace("\n", "\n> ")
                     f.write(f"> {description}\n\n")
 
                 f.write("## Docs\n\n")
@@ -95,7 +100,12 @@ class FileWriter:
                 if not base_url.endswith("/"):
                     base_url += "/"
 
-                for docname in page_order:
+                for item in page_order:
+                    # Handle both old format (str) and new format (tuple)
+                    if isinstance(item, tuple):
+                        docname, _ = item
+                    else:
+                        docname = item
                     title = page_titles.get(docname, docname)
                     f.write(f"- [{title}]({base_url}{docname}.html)\n")
 

tests/test_llms_txt.py

@@ -334,3 +334,396 @@ def test_write_verbose_info_with_baseurl(tmp_path):
 
     assert "- [Home Page](https://example.org/index.html)" in content
     assert "- [About Us](https://example.org/about.html)" in content
+
+
+def test_get_source_suffixes_with_dict():
+    """Test _get_source_suffixes method with dict source_suffix."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with dict source_suffix
+    class MockApp:
+        class Config:
+            source_suffix = {".rst": None, ".md": None, ".txt": None}
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+
+    suffixes = manager._get_source_suffixes()
+    assert set(suffixes) == {".rst", ".md", ".txt"}
+
+
+def test_get_source_suffixes_with_list():
+    """Test _get_source_suffixes method with list source_suffix."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with list source_suffix
+    class MockApp:
+        class Config:
+            source_suffix = [".rst", ".md"]
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+
+    suffixes = manager._get_source_suffixes()
+    assert suffixes == [".rst", ".md"]
+
+
+def test_get_source_suffixes_with_string():
+    """Test _get_source_suffixes method with string source_suffix."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with string source_suffix
+    class MockApp:
+        class Config:
+            source_suffix = ".rst"
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+
+    suffixes = manager._get_source_suffixes()
+    assert suffixes == [".rst"]
+
+
+def test_get_source_suffixes_no_app():
+    """Test _get_source_suffixes method with no app set."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    manager = LLMSFullManager()
+
+    suffixes = manager._get_source_suffixes()
+    assert suffixes == [".rst"]  # Default fallback
+
+
+def test_html_sourcelink_suffix_default():
+    """Test html_sourcelink_suffix defaults to .txt when no app is set."""
+    import tempfile
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    manager = LLMSFullManager()
+    manager.set_config(
+        {
+            "llms_txt_full_filename": "test.txt",
+            "llms_txt_exclude": [],
+            "llms_txt_directives": [],
+        }
+    )
+
+    # Create a temporary directory structure
+    with tempfile.TemporaryDirectory() as tmpdir:
+        outdir = f"{tmpdir}/build"
+        srcdir = f"{tmpdir}/source"
+        sources_dir = f"{outdir}/_sources"
+
+        # Create directories
+        import os
+
+        os.makedirs(sources_dir, exist_ok=True)
+        os.makedirs(srcdir, exist_ok=True)
+
+        # Create a test source file with default .txt suffix
+        test_file = f"{sources_dir}/index.rst.txt"
+        with open(test_file, "w") as f:
+            f.write("Test content")
+
+        # Mock env with minimal required attributes
+        class MockEnv:
+            all_docs = {"index": None}
+            titles = {
+                "index": type("TitleNode", (), {"astext": lambda: "Test Title"})()
+            }
+            toctree_includes = {}
+
+        manager.set_env(MockEnv())
+        manager.set_master_doc("index")
+
+        # Test that it uses .txt as the default suffix
+        manager.combine_sources(outdir, srcdir)
+
+        # Verify the file was found and processed (check if output file exists)
+        output_file = f"{outdir}/test.txt"
+        assert os.path.exists(output_file)
+
+
+def test_html_sourcelink_suffix_custom():
+    """Test html_sourcelink_suffix uses custom value from Sphinx config."""
+    import tempfile
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with custom html_sourcelink_suffix
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = "source"
+            source_suffix = ".rst"
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+    manager.set_config(
+        {
+            "llms_txt_full_filename": "test.txt",
+            "llms_txt_exclude": [],
+            "llms_txt_directives": [],
+        }
+    )
+
+    # Create a temporary directory structure
+    with tempfile.TemporaryDirectory() as tmpdir:
+        outdir = f"{tmpdir}/build"
+        srcdir = f"{tmpdir}/source"
+        sources_dir = f"{outdir}/_sources"
+
+        # Create directories
+        import os
+
+        os.makedirs(sources_dir, exist_ok=True)
+        os.makedirs(srcdir, exist_ok=True)
+
+        # Create a test source file with custom .source suffix
+        test_file = f"{sources_dir}/index.rst.source"
+        with open(test_file, "w") as f:
+            f.write("Test content")
+
+        # Mock env with minimal required attributes
+        class MockEnv:
+            all_docs = {"index": None}
+            titles = {
+                "index": type("TitleNode", (), {"astext": lambda: "Test Title"})()
+            }
+            toctree_includes = {}
+
+        manager.set_env(MockEnv())
+        manager.set_master_doc("index")
+
+        # Test that it uses .source as the custom suffix
+        manager.combine_sources(outdir, srcdir)
+
+        # Verify the file was found and processed
+        output_file = f"{outdir}/test.txt"
+        assert os.path.exists(output_file)
+
+
+def test_html_sourcelink_suffix_with_dot():
+    """Test html_sourcelink_suffix adds dot if missing."""
+    import tempfile
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with html_sourcelink_suffix without leading dot
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = "src"  # No leading dot
+            source_suffix = ".rst"
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+    manager.set_config(
+        {
+            "llms_txt_full_filename": "test.txt",
+            "llms_txt_exclude": [],
+            "llms_txt_directives": [],
+        }
+    )
+
+    # Create a temporary directory structure
+    with tempfile.TemporaryDirectory() as tmpdir:
+        outdir = f"{tmpdir}/build"
+        srcdir = f"{tmpdir}/source"
+        sources_dir = f"{outdir}/_sources"
+
+        # Create directories
+        import os
+
+        os.makedirs(sources_dir, exist_ok=True)
+        os.makedirs(srcdir, exist_ok=True)
+
+        # Create a test source file with .src suffix (dot should be added automatically)
+        test_file = f"{sources_dir}/index.rst.src"
+        with open(test_file, "w") as f:
+            f.write("Test content")
+
+        # Mock env with minimal required attributes
+        class MockEnv:
+            all_docs = {"index": None}
+            titles = {
+                "index": type("TitleNode", (), {"astext": lambda: "Test Title"})()
+            }
+            toctree_includes = {}
+
+        manager.set_env(MockEnv())
+        manager.set_master_doc("index")
+
+        # Test that it adds the dot and finds the file
+        manager.combine_sources(outdir, srcdir)
+
+        # Verify the file was found and processed
+        output_file = f"{outdir}/test.txt"
+        assert os.path.exists(output_file)
+
+
+def test_mixed_source_file_formats():
+    """Test handling of mixed source file formats (.rst, .md, .txt)."""
+    import tempfile
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with multiple source suffixes
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = ".txt"
+            source_suffix = {".rst": None, ".md": None, ".txt": None}
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+    manager.set_config(
+        {
+            "llms_txt_full_filename": "test.txt",
+            "llms_txt_exclude": [],
+            "llms_txt_directives": [],
+        }
+    )
+
+    # Create a temporary directory structure
+    with tempfile.TemporaryDirectory() as tmpdir:
+        outdir = f"{tmpdir}/build"
+        srcdir = f"{tmpdir}/source"
+        sources_dir = f"{outdir}/_sources"
+
+        # Create directories
+        import os
+
+        os.makedirs(sources_dir, exist_ok=True)
+        os.makedirs(srcdir, exist_ok=True)
+
+        # Create test source files with different formats
+        files_to_create = [
+            f"{sources_dir}/page1.rst.txt",
+            f"{sources_dir}/page2.md.txt",
+            f"{sources_dir}/page3.txt.txt",
+        ]
+
+        for test_file in files_to_create:
+            with open(test_file, "w") as f:
+                f.write(f"Content for {os.path.basename(test_file)}")
+
+        # Mock env with all documents
+        class MockEnv:
+            all_docs = {"page1": None, "page2": None, "page3": None}
+            titles = {
+                "page1": type("TitleNode", (), {"astext": lambda: "Page 1"})(),
+                "page2": type("TitleNode", (), {"astext": lambda: "Page 2"})(),
+                "page3": type("TitleNode", (), {"astext": lambda: "Page 3"})(),
+            }
+            toctree_includes = {}
+
+        manager.set_env(MockEnv())
+        manager.set_master_doc("page1")
+
+        # Test that all file formats are found and processed
+        manager.combine_sources(outdir, srcdir)
+
+        # Verify the output file was created and contains content from all formats
+        output_file = f"{outdir}/test.txt"
+        assert os.path.exists(output_file)
+
+        with open(output_file, "r") as f:
+            content = f.read()
+
+        # Should contain content from all three files
+        assert "Content for page1.rst.txt" in content
+        assert "Content for page2.md.txt" in content
+        assert "Content for page3.txt.txt" in content
+
+
+def test_source_suffix_detection_priority():
+    """Test source suffix detection tries formats in correct order for docnames."""
+    import tempfile
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Mock Sphinx app with ordered source suffixes
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = ".txt"
+            source_suffix = [".rst", ".md"]  # rst has priority over md
+
+        config = Config()
+
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
+    manager.set_config(
+        {
+            "llms_txt_full_filename": "test.txt",
+            "llms_txt_exclude": [],
+            "llms_txt_directives": [],
+        }
+    )
+
+    # Create a temporary directory structure
+    with tempfile.TemporaryDirectory() as tmpdir:
+        outdir = f"{tmpdir}/build"
+        srcdir = f"{tmpdir}/source"
+        sources_dir = f"{outdir}/_sources"
+
+        # Create directories
+        import os
+
+        os.makedirs(sources_dir, exist_ok=True)
+        os.makedirs(srcdir, exist_ok=True)
+
+        # Create both .rst and .md versions of the same document
+        # Only create files for the specific docname "index"
+        rst_file = f"{sources_dir}/index.rst.txt"
+        md_file = f"{sources_dir}/index.md.txt"
+
+        with open(rst_file, "w") as f:
+            f.write("RST content for index")
+
+        with open(md_file, "w") as f:
+            f.write("Markdown content for index")
+
+        # Mock env with only the index document
+        class MockEnv:
+            all_docs = {"index": None}
+            titles = {
+                "index": type("TitleNode", (), {"astext": lambda: "Index Page"})()
+            }
+            toctree_includes = {"index": []}
+
+        manager.set_env(MockEnv())
+        manager.set_master_doc("index")
+
+        # Test the priority behavior
+        manager.combine_sources(outdir, srcdir)
+
+        # Check that output file was created
+        output_file = f"{outdir}/test.txt"
+        assert os.path.exists(output_file)
+
+        with open(output_file, "r") as f:
+            content = f.read()
+
+        # The system should prefer RST over MD for the "index" docname
+        # But since both files exist and the second phase adds remaining files,
+        # both will be included. The test verifies that RST appears first
+        # (indicating it was found first in the priority order)
+        assert "RST content for index" in content
+
+        # Find positions to verify order
+        rst_pos = content.find("RST content for index")
+        md_pos = content.find("Markdown content for index")
+
+        # RST should come before MD (due to priority in toctree processing)
+        assert rst_pos < md_pos, "RST content should appear before MD content"