Add notes in the what's new and config sections.

docs/source/config/overview.txt

@@ -286,6 +286,8 b' following algorithm:'
 * If not, the value returned by :func:`IPython.utils.path.get_ipython_dir`
   is used. This function will first look at the :envvar:`IPYTHONDIR`
   environment variable and then default to a platform-specific default.
+  Historical support for the :envvar:`IPYTHON_DIR` environment variable will
+  be removed in a future release.
 
 On posix systems (Linux, Unix, etc.), IPython respects the ``$XDG_CONFIG_HOME``
 part of the `XDG Base Directory`_ specification. If ``$XDG_CONFIG_HOME`` is

docs/source/whatsnew/development.txt

@@ -15,4 +15,7 b' Other new features'
 * **%install_ext**: A new magic function to install an IPython extension from
   a URL. E.g. ``%install_ext https://bitbucket.org/birkenfeld/ipython-physics/raw/d1310a2ab15d/physics.py``.
 
+* The :envvar:`IPYTHON_DIR` environment variable has been deprecated and
+  support for it will be removed in a future release. Please use the
+  :envvar:`IPYTHONDIR` environment variable instead.