update/replace deprecated directives

Author: schmalliso

source/index.txt

@@ -96,16 +96,14 @@ versions of Apache Spark and MongoDB:
    - **November 1, 2016**, `MongoDB Connector for Spark v2.0.0
      <https://www.mongodb.com/products/spark-connector>`_ Released.
 
-.. class:: hidden
-
-   .. toctree::
-      :titlesonly:
-
-      configuration
-      scala-api
-      java-api
-      python-api
-      r-api
-      faq
-      release-notes
-      API Docs <https://www.javadoc.io/doc/org.mongodb.spark/mongo-spark-connector_2.11/{+current-version+}>
+.. toctree::
+   :titlesonly:
+
+   configuration
+   scala-api
+   java-api
+   python-api
+   r-api
+   faq
+   release-notes
+   API Docs <https://www.javadoc.io/doc/org.mongodb.spark/mongo-spark-connector_2.11/{+current-version+}>

source/java-api.txt

@@ -4,7 +4,7 @@ Spark Connector Java Guide
 
 .. default-domain:: mongodb
 
-.. admonition:: Source Code
+.. note:: Source Code
 
    For the source code that combines all of the Java examples, see
    :mongo-spark:`JavaIntroduction.java
@@ -117,12 +117,10 @@ Tutorials
 - :doc:`/java/aggregation`
 - :doc:`/java/datasets-and-sql`
 
-.. class:: hidden
+.. toctree::
+   :titlesonly:
 
-   .. toctree::
-      :titlesonly:
-
-      /java/write-to-mongodb
-      /java/read-from-mongodb
-      /java/aggregation
-      /java/datasets-and-sql
+   /java/write-to-mongodb
+   /java/read-from-mongodb
+   /java/aggregation
+   /java/datasets-and-sql

source/python-api.txt

@@ -10,7 +10,7 @@ Spark Connector Python Guide
    :depth: 2
    :class: singlecol
 
-.. admonition:: Source Code
+.. note:: Source Code
 
    For the source code that contains the examples below, see
    :mongo-spark:`introduction.py
@@ -76,13 +76,11 @@ Tutorials
 - :doc:`/python/aggregation`
 - :doc:`/python/filters-and-sql`
 
-.. class:: hidden
+.. toctree::
+   :titlesonly:
 
-   .. toctree::
-      :titlesonly:
-
-      /python/write-to-mongodb
-      /python/read-from-mongodb
-      /python/aggregation
-      /python/filters-and-sql
+   /python/write-to-mongodb
+   /python/read-from-mongodb
+   /python/aggregation
+   /python/filters-and-sql
 

source/r-api.txt

@@ -4,7 +4,7 @@ Spark Connector R Guide
 
 .. default-domain:: mongodb
 
-.. admonition:: Source Code
+.. note:: Source Code
 
    For the source code that contains the examples below, see
    :mongo-spark:`introduction.R
@@ -67,12 +67,10 @@ Tutorials
 - :doc:`/r/aggregation`
 - :doc:`/r/filters-and-sql`
 
-.. class:: hidden
+.. toctree::
+   :titlesonly:
 
-   .. toctree::
-      :titlesonly:
-
-      /r/write-to-mongodb
-      /r/read-from-mongodb
-      /r/aggregation
-      /r/filters-and-sql
+   /r/write-to-mongodb
+   /r/read-from-mongodb
+   /r/aggregation
+   /r/filters-and-sql

source/scala-api.txt

@@ -4,7 +4,7 @@ Spark Connector Scala Guide
 
 .. default-domain:: mongodb
 
-.. admonition:: Source Code
+.. note:: Source Code
 
    For the source code that contains the examples below, see
    :mongo-spark:`Introduction.scala
@@ -139,13 +139,11 @@ Tutorials
 - :doc:`/scala/datasets-and-sql`
 - :doc:`/scala/streaming`
 
-.. class:: hidden
+.. toctree::
+   :titlesonly:
 
-   .. toctree::
-      :titlesonly:
-   
-      /scala/write-to-mongodb
-      /scala/read-from-mongodb
-      /scala/aggregation
-      /scala/datasets-and-sql
-      /scala/streaming
+   /scala/write-to-mongodb
+   /scala/read-from-mongodb
+   /scala/aggregation
+   /scala/datasets-and-sql
+   /scala/streaming

source/scala/datasets-and-sql.txt

@@ -4,7 +4,7 @@ Datasets and SQL
 
 .. default-domain:: mongodb
 
-.. admonition:: Source Code
+.. note:: Source Code
 
    For the source code that contains the examples below, see
    :mongo-spark:`SparkSQL.scala