Removed the reference guide from the docs.

docs/index.rst

@@ -10,5 +10,4 @@ Also see the `Cython project homepage <http://cython.org/>`_.
    src/quickstart/index
    src/tutorial/index
    src/userguide/index
-   src/reference/index
    src/changes

docs/src/userguide/numpy_tutorial.rst

@@ -76,7 +76,7 @@ However there are several options to automate these steps:
 4. Cython supports distutils so that you can very easily create build scripts
    which automate the process, this is the preferred method for
    Cython implemented libraries and packages.
-   See :ref:`Compiling with distutils <compiling-distutils>`.
+   See :ref:`Basic setup.py <basic_setup.py>`.
 5. Manual compilation (see below)
 
 .. Note::

docs/src/userguide/source_files_and_compilation.rst

@@ -23,6 +23,8 @@ into an extension module.
 The following sub-sections describe several ways to build your
 extension modules, and how to pass directives to the Cython compiler.
 
+.. _compiling_command_line:
+
 Compiling from the command line
 ===============================
 
@@ -97,6 +99,7 @@ that CPython generates for disambiguation, such as
 ``yourmod.cpython-35m-x86_64-linux-gnu.so`` on a regular 64bit Linux installation
 of CPython 3.5.
 
+.. _basic_setup.py:
 
 Basic setup.py
 ===============
@@ -280,6 +283,16 @@ Just as an example, this adds ``mylib`` as library to every extension::
     then the argument to ``create_extension`` must be pickleable.
     In particular, it cannot be a lambda function.
 
+.. _cythonize_arguments:
+
+Cythonize arguments
+-------------------
+
+The function :func:`cythonize` can take extra arguments which will allow you to
+customize your build.
+
+.. autofunction:: Cython.Build.cythonize
+
 
 Multiple Cython Files in a Package
 ===================================
@@ -301,6 +314,8 @@ them through :func:`cythonize`::
     )
 
 
+.. _distributing_cython_modules:
+
 Distributing Cython modules
 ----------------------------
 
@@ -400,6 +415,8 @@ when you try to use them from a dependent package.
 To prevent this, include ``zip_safe=False`` in the arguments to ``setup()``.
 
 
+.. _integrating_multiple_modules:
+
 Integrating multiple modules
 ============================
 
@@ -539,6 +556,8 @@ into the package hierarchy (usually next to the source file) for manual
 reuse, you can pass the option ``inplace=True``.
 
 
+.. _compiling_with_cython_inline:
+
 Compiling with ``cython.inline``
 =================================
 
@@ -554,6 +573,8 @@ Unbound variables are automatically pulled from the surrounding local
 and global scopes, and the result of the compilation is cached for
 efficient re-use.
 
+.. _compiling_with_sage:
+
 Compiling with Sage
 ===================
 
@@ -630,6 +651,8 @@ You can see them also by typing ```%%cython?`` in IPython or a Jupyter notebook.
 ============================================  =======================================================================================================================================
 
 
+.. _compiler_options:
+
 Compiler options
 ----------------
 
@@ -832,6 +855,8 @@ Cython code.  Here is the list of currently supported directives:
     coroutine(s) iterable and thus directly interoperable with yield-from.
 
 
+.. _configurable_optimisations:
+
 Configurable optimisations
 --------------------------
 
@@ -850,6 +875,8 @@ Configurable optimisations
     completely wrong.
     Disabling this option can also reduce the code size.  Default is True.
 
+.. _warnings:
+
 Warnings
 --------
 
@@ -882,6 +909,8 @@ to turn the warning on / off.
    a value type, but could be mininterpreted as declaring two pointers.
 
 
+.. _how_to_set_directives:
+
 How to set directives
 ---------------------