Add source code files to llms-full.txt (#24)

* 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 +1,46 @@
 Changelog
 =========
 
+0.4.0
+-----
+
+- Add support for including source code files with :confval:`llms_txt_code_files` and :confval:`llms_txt_code_base_path` configuration options
+  `#24 <https://github.com/jdillard/sphinx-llms-txt/pull/24>`_
+
+0.3.2
+-----
+
+- Fix image paths to deployed images
+  `#30 <https://github.com/jdillard/sphinx-llms-txt/pull/30>`_
+
+0.3.1
+-----
+
+- Fix issue when ``source_suffix`` equals ``source_link_suffix``
+  `#29 <https://github.com/jdillard/sphinx-llms-txt/pull/29>`_
+
+0.3.0
+-----
+
+- Use first paragraph as default for ``llms_txt_summary``
+  `#22 <https://github.com/jdillard/sphinx-llms-txt/pull/22>`_
+
+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 +1,15 @@
 # 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)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/sphinx-llms-txt.svg)](https://anaconda.org/conda-forge/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 +1,222 @@
+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.
+
+.. _including_code_files:
+
+Including Source Code Files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can include source code files from your project at the end of :confval:`llms_txt_full_filename`.
+
+Use include/exclude syntax to precisely control which files are included:
+
+.. code-block:: python
+
+   llms_txt_code_files = [
+       "+:src/**/*.py",           # Include all Python files in src
+       "-:src/**/__pycache__/**", # Exclude Python cache files
+   ]
+
+Pattern syntax:
+
+- **+:pattern**: Include files matching the pattern. Processed first to collect matching files.
+- **-:pattern**: Exclude files matching the pattern. Applied to filter out unwanted files.
+
+Code files are processed as follows:
+
+- **Glob patterns**: Use standard glob patterns (``*``, ``**``, ``?``) to match files
+- **Relative paths**: Patterns are resolved relative to your Sphinx source directory
+- **Formatting**: Each file is presented with a title and syntax-highlighted code block
+
+.. _customizing_code_paths:
+
+Customizing Code File Paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+By default, the extension automatically detects the relative path from your Sphinx source directory to the git root and strips that prefix from displayed file paths. You can customize this behavior:
+
+.. code-block:: python
+
+   # Manually specify base path to strip
+   llms_txt_code_base_path = "../../"
+
+   # Disable path stripping entirely
+   llms_txt_code_base_path = ""
+
+This helps create cleaner, more readable file paths in the generated documentation.
+
+.. _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 :doc:`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_*"]
+
+   # Source code inclusion with include/exclude patterns
+   llms_txt_code_files = [
+       "+:../../src/**/*.py",           # Include Python files
+       "+:../../config/*.yaml",         # Include config files
+       "-:../../src/**/__pycache__/**", # Exclude cache files
+   ]
+   llms_txt_code_base_path = "../../"

docs/source/changelog.rst

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

docs/source/conf.py

@@ -0,0 +1,106 @@
+#
+# 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_code_files = ["+:../../sphinx_llms_txt/*.py"]
+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 = {
+    "source_repository": "https://github.com/jdillard/sphinx-llms-txt/",
+    "source_branch": "main",
+    "source_directory": "docs/source/",
+}
+
+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 +1,103 @@
+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
+   - **Default**: The first paragraph in the root document, else an empty string
+   - **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
+
+.. confval:: llms_txt_code_files
+
+   - **Type**: list of strings
+   - **Default**: ``[]``
+   - **Description**: A list of glob patterns that appends source code files to :confval:`llms_txt_full_filename`.
+     See :ref:`including_code_files`.
+
+   .. versionadded:: 0.4.0
+
+.. confval:: llms_txt_code_base_path
+
+   - **Type**: string or ``None``
+   - **Default**: ``None`` (auto-detect from git root)
+   - **Description**: Base path to strip from code file paths when displaying titles.
+     When ``None``, automatically detects the relative path from the Sphinx source
+     directory to the git root and strips that prefix from file paths.
+
+   .. versionadded:: 0.4.0

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 +1,34 @@
+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| |Conda 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
+.. |Conda Version| image:: https://img.shields.io/conda/vn/conda-forge/sphinx-llms-txt.svg
+    :target: https://anaconda.org/conda-forge/sphinx-llms-txt
+    :alt: Latest Conda 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__ = "0.4.0"
 
 # Export classes needed by tests
 __all__ = [
@@ -25,9 +25,14 @@ __all__ = [
 # Global manager instance
 _manager = LLMSFullManager()
 
+# Store root document first paragraph
+_root_first_paragraph = ""
+
 
 def doctree_resolved(app: Sphinx, doctree, docname: str):
     """Called when a docname has been resolved to a document."""
+    global _root_first_paragraph
+
     # Extract title from the document
     title = None
     # findall() returns a generator, convert to list to check if it has elements
@@ -38,6 +43,14 @@ def doctree_resolved(app: Sphinx, doctree, docname: str):
     if title:
         _manager.update_page_title(docname, title)
 
+    # Extract first paragraph from root document
+    if docname == app.config.master_doc:
+        for node in doctree.traverse(nodes.paragraph):
+            first_para = node.astext()
+            if first_para:
+                _root_first_paragraph = first_para
+                break
+
 
 def build_finished(app: Sphinx, exception):
     """Called when the build is finished."""
@@ -47,18 +60,24 @@ def build_finished(app: Sphinx, exception):
         _manager.set_master_doc(app.config.master_doc)
         _manager.set_app(app)
 
+        # Get the summary - use configured value or extracted first paragraph
+        summary = app.config.llms_txt_summary
+        if summary is None:
+            summary = _root_first_paragraph
+
         # Set up configuration
         config = {
             "llms_txt_file": app.config.llms_txt_file,
             "llms_txt_filename": app.config.llms_txt_filename,
             "llms_txt_title": app.config.llms_txt_title,
-            "llms_txt_summary": app.config.llms_txt_summary,
+            "llms_txt_summary": summary,
             "llms_txt_full_file": app.config.llms_txt_full_file,
             "llms_txt_full_filename": app.config.llms_txt_full_filename,
             "llms_txt_full_max_size": app.config.llms_txt_full_max_size,
             "llms_txt_directives": app.config.llms_txt_directives,
             "llms_txt_exclude": app.config.llms_txt_exclude,
-            "llms_txt_rm_directives": app.config.llms_txt_rm_directives,
+            "llms_txt_code_files": app.config.llms_txt_code_files,
+            "llms_txt_code_base_path": app.config.llms_txt_code_base_path,
             "html_baseurl": getattr(app.config, "html_baseurl", ""),
         }
         _manager.set_config(config)
@@ -87,15 +106,17 @@ def setup(app: Sphinx) -> Dict[str, Any]:
     app.add_config_value("llms_txt_title", None, "env")
     app.add_config_value("llms_txt_summary", None, "env")
     app.add_config_value("llms_txt_exclude", [], "env")
-    app.add_config_value("llms_txt_rm_directives", False, "env")
+    app.add_config_value("llms_txt_code_files", [], "env")
+    app.add_config_value("llms_txt_code_base_path", None, "env")
 
     # Connect to Sphinx events
     app.connect("doctree-resolved", doctree_resolved)
     app.connect("build-finished", build_finished)
 
-    # Reset manager for each build
-    global _manager
+    # Reset manager and root paragraph for each build
+    global _manager, _root_first_paragraph
     _manager = LLMSFullManager()
+    _root_first_paragraph = ""
 
     return {
         "version": __version__,

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 +38,79 @@ 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:
+            # Avoid duplicate extensions when source_suffix == source_link_suffix
+            if src_suffix == source_link_suffix:
+                candidate_file = sources_dir / f"{docname}{src_suffix}"
+            else:
+                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 +124,12 @@ 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:
@@ -65,20 +140,33 @@ 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
-
-                        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
+                # 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 (
-                                        child_docname != docname
-                                    ):  # Avoid circular references
+                            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())
+
+                    # 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 +176,33 @@ 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

@@ -2,8 +2,10 @@
 Main manager module for sphinx-llms-txt.
 """
 
+import glob
+import subprocess
 from pathlib import Path
-from typing import Any, Dict, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 
 from sphinx.application import Sphinx
 from sphinx.environment import BuildEnvironment
@@ -16,6 +18,104 @@ from .writer import FileWriter
 logger = logging.getLogger(__name__)
 
 
+def _get_git_root(path: Path) -> Optional[Path]:
+    """Get the git root directory for a given path."""
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--show-toplevel"],
+            cwd=path,
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        return Path(result.stdout.strip())
+    except (subprocess.CalledProcessError, FileNotFoundError):
+        return None
+
+
+def _get_language_from_extension(file_path: Path) -> str:
+    """Map file extension to language identifier for code blocks."""
+    extension_map = {
+        ".py": "python",
+        ".js": "javascript",
+        ".jsx": "jsx",
+        ".ts": "typescript",
+        ".tsx": "tsx",
+        ".java": "java",
+        ".c": "c",
+        ".cpp": "cpp",
+        ".cc": "cpp",
+        ".cxx": "cpp",
+        ".h": "c",
+        ".hpp": "cpp",
+        ".cs": "csharp",
+        ".php": "php",
+        ".rb": "ruby",
+        ".go": "go",
+        ".rs": "rust",
+        ".swift": "swift",
+        ".kt": "kotlin",
+        ".scala": "scala",
+        ".sh": "bash",
+        ".bash": "bash",
+        ".zsh": "zsh",
+        ".fish": "fish",
+        ".ps1": "powershell",
+        ".html": "html",
+        ".htm": "html",
+        ".xml": "xml",
+        ".css": "css",
+        ".scss": "scss",
+        ".sass": "sass",
+        ".less": "less",
+        ".json": "json",
+        ".yaml": "yaml",
+        ".yml": "yaml",
+        ".toml": "toml",
+        ".ini": "ini",
+        ".cfg": "ini",
+        ".conf": "ini",
+        ".sql": "sql",
+        ".md": "markdown",
+        ".rst": "rst",
+        ".txt": "text",
+        ".dockerfile": "dockerfile",
+        ".dockerignore": "text",
+        ".gitignore": "text",
+        ".gitattributes": "text",
+        ".editorconfig": "ini",
+        ".makefile": "makefile",
+        ".r": "r",
+        ".R": "r",
+        ".m": "matlab",
+        ".pl": "perl",
+        ".lua": "lua",
+        ".vim": "vim",
+        ".vimrc": "vim",
+        ".proto": "protobuf",
+        ".thrift": "thrift",
+        ".graphql": "graphql",
+        ".gql": "graphql",
+    }
+
+    # Get the extension from the file path
+    ext = file_path.suffix.lower()
+
+    # Handle special cases like Makefile, Dockerfile without extension
+    if not ext:
+        name = file_path.name.lower()
+        if name in ["makefile", "gnumakefile"]:
+            return "makefile"
+        elif name in ["dockerfile", "dockerfile.dev", "dockerfile.prod"]:
+            return "dockerfile"
+        elif name.startswith("dockerfile."):
+            return "dockerfile"
+        else:
+            return "text"
+
+    return extension_map.get(ext, "text")
+
+
 class LLMSFullManager:
     """Manages the collection and ordering of documentation sources."""
 
@@ -56,6 +156,7 @@ 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 +170,7 @@ 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 +189,23 @@ 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
@@ -119,44 +213,69 @@ 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:
+                # Avoid duplicate extensions when source_suffix == source_link_suffix
+                if src_suffix == source_link_suffix:
+                    source_file = sources_dir / f"{docname}{src_suffix}"
+                    expected_suffix = src_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("_", "-")]
+                    source_file = (
+                        sources_dir / f"{docname}{src_suffix}{source_link_suffix}"
+                    )
+                    expected_suffix = f"{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}{expected_suffix}"
+                    )
+            else:
+                logger.warning(
+                    f"sphinx-llms-txt: No source suffix determined for: {docname}"
+                )
 
         # Generate content
         content_parts = []
 
+        # Track code files for later processing
+        code_file_parts = []
+
+        # Count lines in code files (initially 0)
+        code_files_line_count = 0
+
         # Add pages in order
         added_files = set()
-        total_line_count = 0
+        total_line_count = code_files_line_count
         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)
@@ -190,75 +309,118 @@ 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:
+                # Avoid duplicate extensions when source_suffix == source_link_suffix
+                if src_suffix == source_link_suffix:
+                    glob_pattern = f"**/*{src_suffix}"
+                else:
+                    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
-                    )
+            # 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"
                 )
-            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)
+
+            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:
+                    # Avoid duplicate extensions when suffixes match
+                    if src_suffix == source_link_suffix:
+                        combined_suffix = src_suffix
+                    else:
+                        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
 
+        # Process code files at the end if configured
+        if not abort_due_to_max_lines:
+            code_file_parts, processed_file_paths = self._process_code_files()
+            code_files_line_count = sum(
+                part.count("\n") + 1 for part in code_file_parts
+            )
+
+            # Check if adding code files would exceed the maximum line count
+            max_lines = self.config.get("llms_txt_full_max_size")
+            if (
+                max_lines is not None
+                and total_line_count + code_files_line_count > max_lines
+            ):
+                logger.warning(
+                    f"sphinx-llms-txt: Adding code files would exceed max line limit "
+                    f"({max_lines}). Current: {total_line_count}, "
+                    f"Code files: {code_files_line_count}. Skipping code files."
+                )
+            else:
+                # Add source code files section if there are any code files
+                if code_file_parts:
+                    section_header = self._create_code_files_section_header(
+                        processed_file_paths
+                    )
+                    content_parts.append(section_header)
+                    content_parts.extend(code_file_parts)
+                    # Add line count for the section header too
+                    total_line_count += (
+                        code_files_line_count + section_header.count("\n") + 1
+                    )
+
         # Check if line limit was exceeded before creating the file
         max_lines = self.config.get("llms_txt_full_max_size")
         if abort_due_to_max_lines or (
             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 +487,329 @@ 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
+
+    def _process_code_files(self) -> Tuple[List[str], List[Path]]:
+        """Process code files specified in llms_txt_code_files configuration.
+
+        Supports include/exclude patterns with +:/- : prefixes:
+        - '+:pattern' = include files matching pattern
+        - '-:pattern' = exclude files matching pattern
+        - 'pattern' (no prefix) = ignored (no special handling)
+
+        Returns:
+            Tuple of (formatted code block strings, list of processed file paths)
+        """
+        code_file_patterns = self.config.get("llms_txt_code_files", [])
+        if not code_file_patterns:
+            return [], []
+
+        # Parse patterns into include and exclude lists
+        include_patterns = []
+        exclude_patterns = []
+
+        for pattern in code_file_patterns:
+            if pattern.startswith("-:"):
+                exclude_patterns.append(pattern[2:])  # Remove the '-:' prefix
+            elif pattern.startswith("+:"):
+                include_patterns.append(pattern[2:])  # Remove the '+:' prefix
+            else:
+                # No prefix = log warning about ignored pattern
+                logger.warning(
+                    f"sphinx-llms-txt: Code file pattern '{pattern}' ignored."
+                    f"Use '+:{pattern}' to include or '-:{pattern}' to exclude."
+                )
+
+        # If no include patterns specified, nothing to process
+        if not include_patterns:
+            return [], []
+
+        code_parts = []
+        processed_files = set()
+        all_matching_files = set()
+
+        # First, collect all files matching include patterns
+        for pattern in include_patterns:
+            # Resolve pattern relative to source directory
+            if self.srcdir:
+                pattern_path = Path(self.srcdir) / pattern
+            else:
+                pattern_path = Path(pattern)
+
+            # Use glob to find matching files
+            matching_files = glob.glob(str(pattern_path), recursive=True)
+
+            for file_path_str in matching_files:
+                file_path = Path(file_path_str)
+                if file_path.is_file():  # Only add files, not directories
+                    all_matching_files.add(file_path.resolve())
+
+        # Filter out files matching exclude patterns
+        filtered_files = set()
+        for file_path in all_matching_files:
+            should_exclude = False
+
+            for exclude_pattern in exclude_patterns:
+                # Resolve exclude pattern relative to source directory
+                if self.srcdir:
+                    exclude_pattern_path = Path(self.srcdir) / exclude_pattern
+                else:
+                    exclude_pattern_path = Path(exclude_pattern)
+
+                # Check if this file matches the exclude pattern
+                exclude_matches = glob.glob(str(exclude_pattern_path), recursive=True)
+                if str(file_path) in exclude_matches:
+                    should_exclude = True
+                    logger.debug(
+                        f"sphinx-llms-txt: Excluding code file: {file_path} "
+                        f"(matched pattern: {exclude_pattern})"
+                    )
+                    break
+
+            if not should_exclude:
+                filtered_files.add(file_path)
+
+        # Sort files for consistent ordering
+        sorted_files = sorted(filtered_files)
+
+        for file_path in sorted_files:
+            # Skip if already processed (shouldn't happen with set, but safety check)
+            if file_path in processed_files:
+                continue
+
+            try:
+                # Read the file content
+                with open(file_path, "r", encoding="utf-8", errors="ignore") as f:
+                    content = f.read()
+
+                # Get language identifier
+                language = _get_language_from_extension(file_path)
+
+                # Get relative path from source directory for title
+                if self.srcdir:
+                    try:
+                        title = file_path.relative_to(Path(self.srcdir))
+
+                        # Strip base path if configured,
+                        # or auto-detect from git root
+                        base_path = self.config.get("llms_txt_code_base_path")
+                        if base_path is None:
+                            # Auto-detect: try to make path relative to git root
+                            git_root = _get_git_root(Path(self.srcdir))
+                            if git_root:
+                                try:
+                                    # Get srcdir relative to git root
+                                    srcdir_relative = Path(self.srcdir).relative_to(
+                                        git_root
+                                    )
+                                    # Calculate relative path from srcdir to
+                                    # git root
+                                    if srcdir_relative != Path("."):
+                                        # Count directory levels to go up
+                                        up_levels = len(srcdir_relative.parts)
+                                        base_path = "../" * up_levels
+                                    else:
+                                        base_path = None
+                                except ValueError:
+                                    base_path = None
+
+                        if base_path:
+                            title_str = str(title)
+                            if title_str.startswith(base_path):
+                                title = Path(title_str[len(base_path) :])
+                    except ValueError:
+                        # File is not relative to srcdir, use filename
+                        title = file_path.name
+                else:
+                    title = file_path.name
+
+                # Format as code block with equals underline
+                title_str = str(title)
+                equals_line = "=" * len(title_str)
+
+                # Indent the content for reStructuredText code-block directive
+                indented_content = "\n".join(
+                    f"   {line}" if line.strip() else ""
+                    for line in content.splitlines()
+                )
+
+                code_block = f"""
+{title_str}
+{equals_line}
+
+.. code-block:: {language}
+
+{indented_content}"""
+                code_parts.append(code_block)
+
+                processed_files.add(file_path)
+                logger.debug(f"sphinx-llms-txt: Added code file: {title}")
+
+            except Exception as e:
+                logger.warning(
+                    f"sphinx-llms-txt: Error reading code file {file_path}: {e}"
+                )
+                continue
+
+        return code_parts, sorted(processed_files)
+
+    def _create_code_files_section_header(self, file_paths: List[Path] = None) -> str:
+        """Create the section header for source code files.
+
+        Args:
+            file_paths: List of file paths that were added to generate tree view
+
+        Returns:
+            String containing the section header with title, underlines, description,
+            and file tree
+        """
+        section_title = "Source Code Files"
+        star_line = "*" * len(section_title)
+
+        description = "This section contains source code files from the project repository. These files are included to provide implementation context and technical details that complement the documentation above."  # noqa: E501
+
+        header = f"""
+{star_line}
+{section_title}
+{star_line}
+
+{description}"""
+
+        # Add file tree if file paths are provided
+        if file_paths:
+            tree_display = self._generate_file_tree(file_paths)
+            header += f"""
+
+**Files included:**
+
+.. code-block:: text
+
+{tree_display}"""
+
+        return header
+
+    def _generate_file_tree(self, file_paths: List[Path]) -> str:
+        """Generate a tree-like representation of file paths.
+
+        Args:
+            file_paths: List of file paths to display in tree format
+
+        Returns:
+            String containing indented tree representation of the files
+        """
+        if not file_paths:
+            return ""
+
+        # Convert to relative paths if possible and create tree structure
+        tree_data = {}
+
+        for file_path in sorted(file_paths):
+            # Get relative path from source directory for display
+            if self.srcdir:
+                try:
+                    rel_path = file_path.relative_to(Path(self.srcdir))
+
+                    # Apply base path stripping logic similar to code processing
+                    base_path = self.config.get("llms_txt_code_base_path")
+                    if base_path is None:
+                        # Auto-detect: try to make path relative to git root
+                        git_root = _get_git_root(Path(self.srcdir))
+                        if git_root:
+                            try:
+                                # Get srcdir relative to git root
+                                srcdir_relative = Path(self.srcdir).relative_to(
+                                    git_root
+                                )
+                                # Calculate relative path from srcdir to git root
+                                if srcdir_relative != Path("."):
+                                    # Count directory levels to go up
+                                    up_levels = len(srcdir_relative.parts)
+                                    base_path = "../" * up_levels
+                                else:
+                                    base_path = None
+                            except ValueError:
+                                base_path = None
+
+                    if base_path:
+                        rel_path_str = str(rel_path)
+                        if rel_path_str.startswith(base_path):
+                            rel_path = Path(rel_path_str[len(base_path) :])
+
+                except ValueError:
+                    # File is not relative to srcdir, use filename
+                    rel_path = Path(file_path.name)
+            else:
+                rel_path = Path(file_path.name)
+
+            # Build nested dictionary structure
+            parts = rel_path.parts
+            current = tree_data
+            for part in parts[:-1]:  # All but the last part (directories)
+                if part not in current:
+                    current[part] = {}
+                current = current[part]
+
+            # Add the file (last part)
+            if parts:
+                current[parts[-1]] = None  # None indicates it's a file
+
+        # Convert tree structure to string representation
+        lines = []
+        self._format_tree_node(tree_data, lines, "", True)
+
+        # Indent each line for reStructuredText code block
+        indented_lines = [f"   {line}" for line in lines]
+        return "\n".join(indented_lines)
+
+    def _format_tree_node(
+        self, node: dict, lines: List[str], prefix: str, is_root: bool
+    ):
+        """Recursively format tree nodes into lines with proper tree characters.
+
+        Args:
+            node: Dictionary representing the tree structure
+            lines: List to append formatted lines to
+            prefix: Current prefix for indentation and tree characters
+            is_root: Whether this is the root level (no tree characters)
+        """
+        if not node:
+            return
+
+        items = sorted(node.items())
+
+        for i, (name, subtree) in enumerate(items):
+            is_last = i == len(items) - 1
+
+            if is_root:
+                # Root level - no tree characters
+                current_prefix = ""
+                next_prefix = ""
+            else:
+                # Use tree characters
+                current_prefix = prefix + ("└── " if is_last else "├── ")
+                next_prefix = prefix + ("    " if is_last else "│   ")
+
+            lines.append(current_prefix + name)
+
+            # Recursively handle subdirectories
+            if subtree is not None:  # It's a directory
+                self._format_tree_node(subtree, lines, next_prefix, False)

sphinx_llms_txt/processor.py

@@ -50,33 +50,8 @@ class DocumentProcessor:
         # Then process path directives (image, figure, etc.)
         content = self._process_path_directives(content, source_path)
 
-        # Remove directives if configured to do so
-        if self.config.get("llms_txt_rm_directives", False):
-            content = self._remove_directives(content)
-
         return content
 
-    def _remove_directives(self, content: str) -> str:
-        """Remove directives from content.
-
-        Args:
-            content: The source content from which to remove directives
-
-        Returns:
-            Content with all directives removed
-        """
-        # Match any directive pattern (starting with .. followed by ::)
-        directive_pattern = re.compile(r'^\s*\.\.\s+[\w\-]+::.*?$(?:\n\s+.*?$)*',
-                                      re.MULTILINE | re.DOTALL)
-
-        # Replace all directives with an empty string
-        processed_content = directive_pattern.sub('', content)
-
-        # Clean up any consecutive blank lines that might result from directive removal
-        processed_content = re.sub(r'\n{3,}', '\n\n', processed_content)
-
-        return processed_content
-
     def _extract_relative_document_path(
         self, source_path: Path
     ) -> Tuple[Optional[str], Optional[str], Optional[List[str]]]:
@@ -119,8 +94,14 @@ class DocumentProcessor:
         if not base_url:
             return path
 
+        # Ensure base URL ends with slash
         if not base_url.endswith("/"):
             base_url += "/"
+
+        # Remove leading slash from path to avoid double slashes
+        if path.startswith("/"):
+            path = path[1:]
+
         return f"{base_url}{path}"
 
     def _is_absolute_or_url(self, path: str) -> bool:
@@ -162,8 +143,41 @@ class DocumentProcessor:
             prefix = match.group(1)  # The entire directive prefix including whitespace
             path = match.group(3).strip()  # The path argument
 
-            # Only process relative paths, not absolute paths or URLs
-            if not self._is_absolute_or_url(path):
+            # Handle URLs and data URIs - leave unchanged
+            if path.startswith(("http://", "https://", "data:")):
+                return match.group(0)
+
+            # For ALL paths, check if image exists in _images first
+            # Extract filename from the path
+            filename = os.path.basename(path)
+
+            # Check if image exists in _images directory
+            # First determine the build directory from source_path
+            build_dir = None
+            if "_sources" in str(source_path):
+                # Extract build directory (parent of _sources)
+                path_parts = str(source_path).split("_sources/")
+                if len(path_parts) > 1:
+                    build_dir = path_parts[0].rstrip("/")
+
+            # If we can determine the build directory, check if image exists in _images
+            if build_dir:
+                images_path = os.path.join(build_dir, "_images", filename)
+                if os.path.exists(images_path):
+                    # Image exists in _images, use _images path
+                    full_path = f"/_images/{filename}"
+                    # Add base URL if configured
+                    full_path = self._add_base_url(full_path, base_url)
+                    return f"{prefix}{full_path}"
+
+            # Image doesn't exist in _images, handle based on path type
+            # Handle absolute paths (starting with /) - add base URL if configured
+            if path.startswith("/"):
+                # Add base URL to absolute paths if configured
+                full_path = self._add_base_url(path, base_url)
+                return f"{prefix}{full_path}"
+
+            # Handle relative paths with original logic for backward compatibility
             # Special case for test files
             if is_test:
                 # Add subdir/ prefix to match test expectations
@@ -193,9 +207,7 @@ class DocumentProcessor:
                     elif rel_doc_dir:
                         # Join with the original path to form full path relative
                         # to srcdir
-                            full_path = os.path.normpath(
-                                os.path.join(rel_doc_dir, path)
-                            )
+                        full_path = os.path.normpath(os.path.join(rel_doc_dir, path))
                     else:
                         full_path = path
 
@@ -205,7 +217,12 @@ class DocumentProcessor:
                     # Return the updated directive with the full path
                     return f"{prefix}{full_path}"
 
-            # If we couldn't resolve the path or it's already absolute, return unchanged
+            # Fallback for relative paths - add base URL if configured
+            else:
+                full_path = self._add_base_url(path, base_url)
+                return f"{prefix}{full_path}"
+
+            # If we couldn't resolve the path, return unchanged
             return match.group(0)
 
         # Replace directive paths in the content

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 +86,13 @@ class FileWriter:
                 # Add description if available
                 description = self.config.get("llms_txt_summary", "")
                 if description:
+                    # Trim leading and trailing whitespace
+                    description = description.strip()
+                    if description:
+                        # Only add blockquote if description is not empty
+                        # 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 +102,12 @@ 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

@@ -336,42 +336,661 @@ def test_write_verbose_info_with_baseurl(tmp_path):
     assert "- [About Us](https://example.org/about.html)" in content
 
 
-def test_remove_directives():
-    """Test removing directives from content."""
-    # Create a processor with remove_directives enabled
-    config = {"llms_txt_rm_directives": True}
-    processor = DocumentProcessor(config)
+def test_get_source_suffixes_with_dict():
+    """Test _get_source_suffixes method with dict source_suffix."""
+    from sphinx_llms_txt.manager import LLMSFullManager
 
-    # Test content with various directives
-    content = """This is a test document.
+    # Mock Sphinx app with dict source_suffix
+    class MockApp:
+        class Config:
+            source_suffix = {".rst": None, ".md": None, ".txt": None}
 
-.. image:: /path/to/image.jpg
-   :alt: An example image
-   :width: 100%
+        config = Config()
 
-This is a paragraph after the image.
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
 
-.. note::
-   This is a note.
+    suffixes = manager._get_source_suffixes()
+    assert set(suffixes) == {".rst", ".md", ".txt"}
 
-.. code-block:: python
 
-   def hello_world():
-       print("Hello, world!")
+def test_get_source_suffixes_with_list():
+    """Test _get_source_suffixes method with list source_suffix."""
+    from sphinx_llms_txt.manager import LLMSFullManager
 
-Final paragraph."""
+    # Mock Sphinx app with list source_suffix
+    class MockApp:
+        class Config:
+            source_suffix = [".rst", ".md"]
 
-    processed_content = processor._remove_directives(content)
+        config = Config()
 
-    # Check that directives are removed
-    assert ".. image::" not in processed_content
-    assert ".. note::" not in processed_content
-    assert ".. code-block::" not in processed_content
+    manager = LLMSFullManager()
+    manager.set_app(MockApp())
 
-    # Check that regular content is preserved
-    assert "This is a test document." in processed_content
-    assert "This is a paragraph after the image." in processed_content
-    assert "Final paragraph." in processed_content
+    suffixes = manager._get_source_suffixes()
+    assert suffixes == [".rst", ".md"]
 
-    # Check that there are no excessive blank lines
-    assert "\n\n\n" not in processed_content
+
+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"
+
+
+def test_summary_default_uses_first_paragraph():
+    """
+    Test that summary defaults to first paragraph of root document when not configured.
+    """
+    from docutils import nodes
+    from docutils.frontend import OptionParser
+    from docutils.parsers.rst import Parser
+    from docutils.utils import new_document
+
+    from sphinx_llms_txt import build_finished, doctree_resolved
+
+    # Create a proper document with settings
+    settings = OptionParser(components=(Parser,)).get_default_values()
+    doctree = new_document("<rst-doc>", settings)
+
+    title = nodes.title(text="Test Title")
+    paragraph = nodes.paragraph(
+        text="This is the first paragraph that should be used as summary."
+    )
+    doctree.append(title)
+    doctree.append(paragraph)
+
+    # Mock Sphinx app
+    class MockApp:
+        class Config:
+            master_doc = "index"
+            llms_txt_summary = None  # Not configured
+            llms_txt_file = True
+            llms_txt_filename = "llms.txt"
+            llms_txt_title = None
+            llms_txt_full_file = True
+            llms_txt_full_filename = "llms-full.txt"
+            llms_txt_full_max_size = None
+            llms_txt_directives = []
+            llms_txt_exclude = []
+            llms_txt_code_files = []
+            llms_txt_code_base_path = None
+            html_baseurl = ""
+
+        config = Config()
+        outdir = "/tmp/build"
+        srcdir = "/tmp/source"
+
+        class Env:
+            titles = {
+                "index": type("TitleNode", (), {"astext": lambda self: "Test Title"})()
+            }
+
+        env = Env()
+
+    app = MockApp()
+
+    # Reset the global state
+    import sphinx_llms_txt
+
+    sphinx_llms_txt._root_first_paragraph = ""
+
+    # Call doctree_resolved to extract the first paragraph
+    doctree_resolved(app, doctree, "index")
+
+    # Verify the first paragraph was extracted
+    assert (
+        sphinx_llms_txt._root_first_paragraph
+        == "This is the first paragraph that should be used as summary."
+    )
+
+    # Mock the manager methods to avoid actual file operations
+    original_combine_sources = sphinx_llms_txt._manager.combine_sources
+    sphinx_llms_txt._manager.combine_sources = lambda outdir, srcdir: None
+
+    # Call build_finished and verify the summary is set correctly
+    build_finished(app, None)
+
+    # Check that the summary was properly configured
+    assert (
+        sphinx_llms_txt._manager.config["llms_txt_summary"]
+        == "This is the first paragraph that should be used as summary."
+    )
+
+    # Restore original method
+    sphinx_llms_txt._manager.combine_sources = original_combine_sources
+
+
+def test_code_files_include_exclude_patterns(tmp_path):
+    """Test the +/- pattern syntax for llms_txt_code_files configuration."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Create test directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+
+    docs_dir = src_dir / "docs"
+    docs_dir.mkdir()
+
+    cache_dir = docs_dir / "__pycache__"
+    cache_dir.mkdir()
+
+    # Create test files
+    (docs_dir / "example.rst").write_text("Example RST content")
+    (docs_dir / "guide.rst").write_text("Guide RST content")
+    (docs_dir / "backup.bak").write_text("Backup file content")
+    (cache_dir / "compiled.pyc").write_text("Compiled Python")
+
+    # Create manager and set source directory
+    manager = LLMSFullManager()
+    manager.srcdir = str(src_dir)
+
+    # Test configuration with include/exclude patterns
+    config = {
+        "llms_txt_code_files": [
+            "+:docs/**/*.rst",  # Include all RST files in docs
+            "-:docs/**/__pycache__/**",  # Exclude pycache files
+            "-:docs/**/*.bak",  # Exclude backup files
+        ]
+    }
+    manager.set_config(config)
+
+    # Process code files
+    code_parts, _ = manager._process_code_files()
+
+    # Verify we have the expected number of files
+    assert len(code_parts) == 2, f"Expected 2 files, got {len(code_parts)}"
+
+    # Extract file titles from code blocks
+    titles = []
+    for part in code_parts:
+        lines = part.strip().split("\n")
+        if lines:
+            titles.append(lines[0])
+
+    # Verify expected files are included
+    assert "docs/example.rst" in titles
+    assert "docs/guide.rst" in titles
+
+    # Verify excluded files are not present
+    content = "\n".join(code_parts)
+    assert "backup.bak" not in content
+    assert "__pycache__" not in content
+    assert "compiled.pyc" not in content
+
+
+def test_code_files_exclude_only_patterns(tmp_path):
+    """Test that exclude-only patterns result in no files being included."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Create test directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+
+    docs_dir = src_dir / "docs"
+    docs_dir.mkdir()
+
+    # Create test files
+    (docs_dir / "example.rst").write_text("Example RST content")
+
+    # Create manager and set source directory
+    manager = LLMSFullManager()
+    manager.srcdir = str(src_dir)
+
+    # Test configuration with only exclude patterns
+    config = {
+        "llms_txt_code_files": [
+            "-:docs/**/*.rst",  # Only exclude pattern, no includes
+        ]
+    }
+    manager.set_config(config)
+
+    # Process code files
+    code_parts, _ = manager._process_code_files()
+
+    # Should have no files with exclude-only patterns
+    assert len(code_parts) == 0, "Should have no files with exclude-only patterns"
+
+
+def test_code_files_no_prefix_patterns(tmp_path):
+    """Test that patterns without prefix are ignored."""
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Create test directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+
+    docs_dir = src_dir / "docs"
+    docs_dir.mkdir()
+
+    # Create test files
+    (docs_dir / "example.rst").write_text("Example RST content")
+    (docs_dir / "backup.bak").write_text("Backup file content")
+
+    # Create manager and set source directory
+    manager = LLMSFullManager()
+    manager.srcdir = str(src_dir)
+
+    # Test configuration with no prefix (should be ignored)
+    config = {
+        "llms_txt_code_files": [
+            "docs/**/*.rst",  # No prefix = ignored
+            "+:docs/**/*.rst",  # Include RST files
+            "-:docs/**/*.bak",  # Exclude backup files
+        ]
+    }
+    manager.set_config(config)
+
+    # Process code files
+    code_parts, _ = manager._process_code_files()
+
+    # Should include RST files (from +: pattern) and exclude BAK files (from -: pattern)
+    assert len(code_parts) == 1, "Should include RST files and exclude BAK files"
+
+    content = "\n".join(code_parts)
+    assert "Example RST content" in content
+    assert "backup.bak" not in content
+
+
+def test_code_files_ignored_patterns(tmp_path, caplog):
+    """Test that patterns without +: or -: prefix log a warning and are ignored."""
+    from unittest.mock import patch
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Create test directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+
+    docs_dir = src_dir / "docs"
+    docs_dir.mkdir()
+
+    # Create test files
+    (docs_dir / "example.rst").write_text("Example RST content")
+
+    # Use a mock to capture the warning message directly
+    captured_warnings = []
+
+    def capture_warning(message, *args, **kwargs):
+        captured_warnings.append(message)
+
+    # Patch the logger to capture warnings
+    with patch("sphinx_llms_txt.manager.logger.warning", side_effect=capture_warning):
+        # Create manager and set source directory
+        manager = LLMSFullManager()
+        manager.srcdir = str(src_dir)
+
+        # Test configuration with only no-prefix patterns (should result in no files)
+        config = {
+            "llms_txt_code_files": [
+                "docs/**/*.rst",  # No prefix = ignored with warning
+            ]
+        }
+        manager.set_config(config)
+
+        # Process code files
+        code_parts, _ = manager._process_code_files()
+
+    # Should have no files since the pattern without prefix is ignored
+    assert (
+        len(code_parts) == 0
+    ), "Should have no files when only using patterns without prefix"
+
+    # Check that a warning was logged
+    assert (
+        len(captured_warnings) == 1
+    ), f"Expected 1 warning, got {len(captured_warnings)}"
+    assert (
+        "Code file pattern 'docs/**/*.rst' ignored." in captured_warnings[0]
+    ), f"Warning message should contain expected text. Got: {captured_warnings[0]}"

tests/test_path_directives.py

@@ -102,7 +102,7 @@ def test_process_path_directives_with_html_baseurl(tmp_path):
 
 
 def test_process_path_directives_absolute_urls(tmp_path):
-    """Test that absolute URLs are not modified."""
+    """Test that absolute URLs are not modified but absolute paths get base URL."""
     # Create a processor
     config = {
         "llms_txt_directives": [],
@@ -127,10 +127,17 @@ def test_process_path_directives_absolute_urls(tmp_path):
     with open(source_file, "w", encoding="utf-8") as f:
         f.write(source_content)
 
-    # Process the directives (should remain unchanged)
+    # Process the directives
     processed_content = processor._process_path_directives(source_content, source_file)
 
-    assert processed_content == source_content
+    # Expected: URLs and data URIs unchanged, absolute paths get base URL
+    expected_content = (
+        ".. image:: https://othersite.com/images/test.png\n"
+        ".. image:: https://example.com/docs/absolute/path/image.png\n"
+        ".. image:: data:image/png;base64,iVBORw0KG...\n"
+    )
+
+    assert processed_content == expected_content
 
 
 def test_process_path_directives_custom_directives(tmp_path):
@@ -251,3 +258,149 @@ def test_process_content_end_to_end(tmp_path):
     )
 
     assert processed_content == expected_content
+
+
+def test_process_path_directives_images_directory(tmp_path):
+    """Test that _images directory paths are handled correctly."""
+    # Create a processor with base URL
+    config = {
+        "llms_txt_directives": [],
+        "html_baseurl": "https://example.com/docs",
+    }
+    processor = DocumentProcessor(config)
+
+    # Create source directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+    processor.srcdir = str(src_dir)
+
+    # Create _sources directory to mimic Sphinx output
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+    sources_dir = build_dir / "_sources"
+    sources_dir.mkdir()
+
+    # Create a source file with various _images directory paths
+    source_content = (
+        "Some content.\n"
+        ".. image:: _images/test.png\n"  # Relative _images should become /_images
+        ".. image:: /_images/absolute.png\n"  # Absolute _images should get base URL
+        ".. figure:: _images/figure.png\n"  # Test with figure directive too
+        "   :alt: A test figure\n"
+        ".. image:: images/normal.png\n"  # Normal relative path should be unchanged
+    )
+
+    # Create source file in sources directory to simulate Sphinx build output
+    source_file = sources_dir / "page.txt"
+    with open(source_file, "w", encoding="utf-8") as f:
+        f.write(source_content)
+
+    # Process the directives
+    processed_content = processor._process_path_directives(source_content, source_file)
+
+    # Expected: _images paths should be converted and get base URL
+    expected_content = (
+        "Some content.\n"
+        ".. image:: https://example.com/docs/_images/test.png\n"
+        ".. image:: https://example.com/docs/_images/absolute.png\n"
+        ".. figure:: https://example.com/docs/_images/figure.png\n"
+        "   :alt: A test figure\n"
+        ".. image:: https://example.com/docs/images/normal.png\n"
+    )
+
+    assert processed_content == expected_content
+
+
+def test_process_path_directives_images_directory_no_baseurl(tmp_path):
+    """
+    Test that _images directory paths work correctly without base URL.
+    Only converts when image exists.
+    """
+    # Create a processor without base URL
+    config = {
+        "llms_txt_directives": [],
+        "html_baseurl": "",
+    }
+    processor = DocumentProcessor(config)
+
+    # Create source directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+    processor.srcdir = str(src_dir)
+
+    # Create _sources directory to mimic Sphinx output
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+    sources_dir = build_dir / "_sources"
+    sources_dir.mkdir()
+
+    # Create _images directory and one test image
+    images_dir = build_dir / "_images"
+    images_dir.mkdir()
+    (images_dir / "test.png").write_text("fake image content")
+    # Note: absolute.png is not created, so it won't be converted
+
+    # Create a source file with _images directory paths
+    source_content = (
+        ".. image:: _images/test.png\n"  # Should become /_images (image exists)
+        ".. image:: /_images/absolute.png\n"  # Should stay unchanged (absolute path)
+    )
+
+    # Create source file in sources directory to simulate Sphinx build output
+    source_file = sources_dir / "page.txt"
+    with open(source_file, "w", encoding="utf-8") as f:
+        f.write(source_content)
+
+    # Process the directives
+    processed_content = processor._process_path_directives(source_content, source_file)
+
+    # Expected: only test.png gets converted because it exists in _images
+    expected_content = (
+        ".. image:: /_images/test.png\n"  # Converted because image exists
+        ".. image:: /_images/absolute.png\n"  # Absolute path unchanged
+    )
+
+    assert processed_content == expected_content
+
+
+def test_process_path_directives_all_absolute_paths_get_baseurl(tmp_path):
+    """Test that all absolute paths (starting with /) get base URL prepended."""
+    # Create a processor with base URL
+    config = {
+        "llms_txt_directives": [],
+        "html_baseurl": "https://mysite.com/docs/",
+    }
+    processor = DocumentProcessor(config)
+
+    # Create source directory structure
+    src_dir = tmp_path / "src"
+    src_dir.mkdir()
+    processor.srcdir = str(src_dir)
+
+    # Create a source file with various absolute paths
+    source_content = (
+        ".. image:: /static/images/logo.png\n"
+        ".. figure:: /assets/diagrams/flow.svg\n"
+        ".. image:: /media/photos/team.jpg\n"
+        "   :alt: Team photo\n"
+        ".. image:: relative/path.png\n"  # This should still get normal processing
+    )
+
+    # Create source file
+    source_file = src_dir / "page.txt"
+    with open(source_file, "w", encoding="utf-8") as f:
+        f.write(source_content)
+
+    # Process the directives
+    processed_content = processor._process_path_directives(source_content, source_file)
+
+    # Expected: All absolute paths get base URL prepended
+    expected_content = (
+        ".. image:: https://mysite.com/docs/static/images/logo.png\n"
+        ".. figure:: https://mysite.com/docs/assets/diagrams/flow.svg\n"
+        ".. image:: https://mysite.com/docs/media/photos/team.jpg\n"
+        "   :alt: Team photo\n"
+        ".. image:: https://mysite.com/docs/relative/path.png\n"
+    )
+
+    assert processed_content == expected_content