Sphinx does not recognize subfolders

Question

I'm new in using Sphinx. I'm able to create HTML documentations as long as my files are in the source top folder.

As soon as I'm putting them in a subfolder in the source directory, Sphinx does not include the document into the build. Sphinx tells me after generating that the test document is not included. So, it sees the file but does not include it.

Did I miss anything? Do I have to specify any subfolders in the index.rst file or in the config.py?

My index.rst file:

Welcome to python help's documentation!
=======================================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   test

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

My config.py file:

# -*- coding: utf-8 -*-
#
# python help documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 31 18:39:52 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))


# -- 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 = []

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'python help'
copyright = u'2017, Stephan'
author = u'Stephan'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = u'0.0.01'
# The full version, including alpha/beta/rc tags.
release = u'0.0.01'

# 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 = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False


# -- 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 = 'alabaster'

# 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 = {}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']


# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'pythonhelpdoc'


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'pythonhelp.tex', u'python help Documentation',
     u'Stephan', 'manual'),
]


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'pythonhelp', u'python help Documentation',
     [author], 1)
]


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'pythonhelp', u'python help Documentation',
     author, 'pythonhelp', 'One line description of project.',
     'Miscellaneous'),
]

Answer 1

You need to include the relative path to the .rst source file in the subdirectory.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   test
   dir1/file
   dir2/*

In dir1 only the file named file.rst would be included in the TOC. You can exclude files in there, too.

In dir2 all files would be included in the TOC via globbing syntax.

For further information, see documentation of the toctree directive.