Remove unnecessary and mostly documentation links

Why each part was removed:

``` RestructuredText

Contents:  # No contents so this isn't needed.

.. toctree::  # No included files so this isn't needed.
   :maxdepth: 2  # No included files so this isn't needed.



Indices and tables
==================

* :ref:`genindex`  # No indexes specified so this isn't needed
* :ref:`modindex`  # No module indexes specified so this isn't needed
* :ref:`search`  # Search is better done in left RTD full-text side-bar
```