Fix errors with links on the index page and references to deleted documents.

doc/index.txt

@@ -81,8 +81,8 @@ installation and configuration, see :ref:`installing Theano <install>`.
 
      <a href="https://crate.io/packages/Theano/"><img src="https://pypip.in/d/Theano/badge.png" alt="Number of PyPI downloads" /></a>&nbsp;
 
-  .. _available on PyPI: http://pypi.python.org/pypi/Theano
-  .. _Related Projects: https://github.com/Theano/Theano/wiki/Related-projects
+.. _available on PyPI: http://pypi.python.org/pypi/Theano
+.. _Related Projects: https://github.com/Theano/Theano/wiki/Related-projects
 
 Citing Theano
 ==============
@@ -95,7 +95,7 @@ required) to cite the following two papers:
   `"Theano: new features and speed improvements"
   <http://arxiv.org/pdf/1211.5590.pdf>`_.
   NIPS 2012 deep learning workshop. (`BibTex
-  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/551/bibtex>`_)
+  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/551/bibtex>`__)
 
 * J. Bergstra, O. Breuleux, F. Bastien, P. Lamblin, R.
   Pascanu, G. Desjardins, J. Turian, D. Warde-Farley and Y.
@@ -103,7 +103,7 @@ required) to cite the following two papers:
   <http://www.iro.umontreal.ca/~lisa/pointeurs/theano_scipy2010.pdf>`_.
   *Proceedings of the Python for Scientific Computing Conference (SciPy)
   2010. June 30 - July 3, Austin, TX* (`BibTeX
-  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/461/bibtex>`_)
+  <http://www.iro.umontreal.ca/~lisa/publications2/index.php/export/publication/461/bibtex>`__)
 
 Theano is primarily developed by academics, and so citations matter a lot to
 us. As an added benefit, you increase Theano's exposure and potential user
@@ -183,7 +183,6 @@ Community
    glossary
    links
    internal/index
-   examples/index
    proposals/index
    acknowledgement
    LICENSE

doc/sandbox/index2.txt

@@ -12,6 +12,5 @@ Advanced Topics (under construction)
     compilation
     ccodegen
     function
-    module
     debugging_with_stepmode