Fix doc build (#3126)

* Fix doc build

ReadTheDocs build has been broken for a while due to incompatibilities between
commonmark, recommonmark, and sphinx. See:
* "Recommonmark not working with Sphinx 1.6"
  https://github.com/rtfd/recommonmark/issues/73
* "CommonMark 0.6.0 breaks compatibility"
  https://github.com/rtfd/recommonmark/issues/24
For now, we fix the versions to get the build working again

* Fix search bar

doc/_static/xgboost-theme/layout.html

@@ -56,7 +56,7 @@
       };
     </script>
 
-    {% for name in ['jquery.js', 'underscore.js', 'doctools.js', 'searchtools.js'] %}
+    {% for name in ['jquery.js', 'underscore.js', 'doctools.js', 'searchtools-new.js'] %}
     <script type="text/javascript" src="{{ pathto('_static/' + name, 1) }}"></script>
     {% endfor %}