Clean up: refs (#654)

Author: rachel-mack

source/connection/connect.txt

@@ -295,8 +295,7 @@ check the following items in your code:
 
 - The credentials for the authentication mechanism that you specified are
   correct. To learn how to specify your credentials, see the
-  :ref:`authentication-mechanisms` and :ref:`enterprise-authentication-mechanisms`
-  guides.
+  :ref:`authentication-mechanisms` guide.
 
 - The name of the authentication database that you specified is correct. To
   learn how to set up the users and roles for your MongoDB deployment, see

source/connection/connection-options.txt

@@ -193,8 +193,8 @@ parameters of the connection URI to specify the behavior of the client.
 
    * - **authMechanism**
      - string
-     - Specifies the :doc:`authentication mechanism
-       </security/auth>` that the driver uses if a credential
+     - Specifies the :ref:`authentication mechanism
+       <java-authentication-mechanisms>` that the driver uses if a credential
        was supplied.
 
        | **Default**: By default, the client picks the most secure

source/connection/mongoclientsettings.txt

@@ -112,7 +112,7 @@ connection behavior:
      - Sets the :ref:`command listeners <command-events-java>`.
 
    * - ``compressorList()``
-     - Sets the :ref:`compressors <compression>` to use for compressing
+     - Sets the :ref:`compressors <java-compression>` to use for compressing
        messages to the server.
 
    * - ``credential()``
@@ -162,7 +162,7 @@ Example
 
 This example demonstrates specifying a ``ConnectionString``:
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin ConnectionString
    :end-before: end ConnectionString
    :language: java
@@ -290,7 +290,7 @@ Example
 This example specifies for the driver to connect directly to a server,
 regardless of the type of MongoDB cluster it's a part of:
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin ClusterSettings
    :end-before: end ClusterSettings
    :language: java
@@ -380,7 +380,7 @@ This example specifies the following driver behavior in a pool of
 - The thread to wait at most ``10 SECONDS`` for an available connection
 - To have at most ``200`` connections associated with the pool
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin ConnectionPoolSettings
    :end-before: end ConnectionPoolSettings
    :language: java
@@ -417,7 +417,7 @@ Example
 This example specifies that the maximum number of characters for a single log
 message is set to ``5000`` characters.
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin LoggerSettings
    :end-before: end LoggerSettings
    :language: java
@@ -474,7 +474,7 @@ This example specifies the following driver behavior in a MongoDB deployment:
   ``700 MILLISECONDS``
 - The cluster monitor to attempt reaching a server every ``15 SECONDS``
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin ServerSettings
    :end-before: end ServerSettings
    :language: java
@@ -545,7 +545,7 @@ This example specifies the following driver behavior in a MongoDB socket:
 - To connect to an available socket within ``10 SECONDS``
 - To read from an available socket within ``15 SECONDS``
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin SocketSettings
    :end-before: end SocketSettings
    :language: java
@@ -593,7 +593,7 @@ Example
 This example specifies for the driver to enable TLS/SSL when connecting
 to MongoDB:
 
-.. literalinclude:: /includes/fundamentals/code-snippets/mcs.java
+.. literalinclude:: /includes/fundamentals/code-snippets/MCSettings.java
    :start-after: begin SslSettings
    :end-before: end SslSettings
    :language: java

source/crud/builders/aggregates.txt

@@ -1,3 +1,5 @@
+.. _aggregates-builders:
+
 ===================
 Aggregates Builders
 ===================
@@ -17,9 +19,7 @@ Aggregates Builders
 
 .. toctree::
 
-   Atlas Vector Search </builders/vector-search>
-
-.. _aggregates-builders:
+   Atlas Vector Search </atlas-vector-search>
 
 Overview
 --------
@@ -90,7 +90,7 @@ Project
 
 Use the ``project()`` method to create a :manual:`$project </reference/operator/aggregation/project/>`
 pipeline stage that project specified document fields. Field projection
-in aggregation follows the same rules as :doc:`field projection in queries </crud/read-operations/project>`.
+in aggregation follows the same rules as :ref:`field projection in queries <java-fundamentals-project>`.
 
 .. tip::
 

source/crud/builders/filters.txt

@@ -1,26 +1,24 @@
+.. _filters-builders:
+
 ================
 Filters Builders
 ================
 
-
-
 .. contents:: On this page
    :local:
    :backlinks: none
    :depth: 2
    :class: singlecol
 
-.. _filters-builders:
-
 Overview 
 --------
 
 In this guide, you can learn how to use **builders** to specify
 **filters** for your queries in the MongoDB Java driver.
 
 Builders are classes provided by the MongoDB Java driver that help you
-construct :ref:`BSON <bson>` objects. To learn more, see our :doc:`guide
-on builders </builders/>`. 
+construct :ref:`BSON <bson>` objects. To learn more, see our :ref:`guide
+on builders <java-builders>`. 
 
 Filters are the operations MongoDB uses to limit your results to what
 you want to see. 

source/crud/builders/indexes.txt

@@ -1,22 +1,20 @@
+.. _indexes-builders:
+
 ================
 Indexes Builders
 ================
 
-
-
 .. contents:: On this page
    :local:
    :backlinks: none
    :depth: 2
    :class: singlecol
 
-.. _indexes-builders:
-
 Overview 
 --------
 
 In this guide, you can learn how to specify **indexes** using
-:doc:`builders </builders/>` in the MongoDB Java driver.
+:ref:`builders <java-builders>` in the MongoDB Java driver.
 The ``Indexes`` builder provides helper methods for constructing the
 following types of indexes:  
 
@@ -29,7 +27,7 @@ following types of indexes:
 
 Indexes store a subset of the collection’s data set. The index stores
 the value of a specific field or set of fields, ordered by the value of
-the field. See our guide on :doc:`Indexes </fundamentals/indexes>` for
+the field. See our guide on :ref:`Indexes <java-fundamentals-indexes>` for
 examples of queries covered by indexes. 
 
 The ``Indexes`` class provides static factory methods for all the MongoDB index types.

source/crud/builders/projections.txt

@@ -1,22 +1,20 @@
+.. _projections-builders:
+
 ====================
 Projections Builders
 ====================
 
-
-
 .. contents:: On this page
    :local:
    :backlinks: none
    :depth: 2
    :class: singlecol
 
-.. _projections-builders:
-
 Overview
 --------
 
 In this guide, you can learn how to specify **projections** using
-:doc:`builders </builders/>` in the MongoDB Java driver.
+:ref:`builders <java-builders>` in the MongoDB Java driver.
 
 MongoDB supports **field projection**, specifying which fields to include and exclude when returning results from a
 query. Projection in MongoDB follows some basic rules:

source/crud/builders/sort.txt

@@ -1,3 +1,5 @@
+.. _sorts-builders:
+
 ==============
 Sorts Builders
 ==============
@@ -15,8 +17,6 @@ Sorts Builders
    :depth: 2
    :class: singlecol
 
-.. _sorts-builders:
-
 Overview
 --------
 
@@ -31,15 +31,15 @@ examples of sort criteria are:
 * Alphabetical order by first name 
 
 Builders are classes provided by the MongoDB Java driver that help you
-construct :ref:`BSON <bson>` objects. To learn more, see our :doc:`guide
-on builders </builders/>`. 
+construct :ref:`BSON <bson>` objects. To learn more, see our :ref:`guide
+on builders <java-builders>`. 
 
 You should read this guide if you would like to use builders to specify sort
 criteria for your queries.
 
 If you want to learn the fundamentals of sorting in the MongoDB Java
 driver, consider reading our
-:doc:`guide on sorting </crud/read-operations/sort/>`.
+:ref:`guide on sorting <java-fundamentals-sort>`.
 
 .. _sorts-builders-sort-sample:
 
@@ -63,7 +63,7 @@ criteria operators supported by MongoDB. These methods return a ``Bson`` object
 that you can pass to the  ``sort()`` method of a ``FindIterable`` instance or to 
 ``Aggregates.sort()``. If you want to learn more about the ``Aggregates``
 class, see our 
-:doc:`guide on the Aggregates builder </builders/aggregates>`.
+:ref:`guide on the Aggregates builder <aggregates-builders>`.
 
 For more information about the classes and interfaces in this section, see the
 following API Documentation:

source/crud/collations.txt

@@ -71,7 +71,7 @@ order as shown below:
 How to Specify Collations
 -------------------------
 
-MongoDB supports collations on most :doc:`CRUD operations </fundamentals/crud>`
+MongoDB supports collations on most :ref:`CRUD operations <java-crud-operations>`
 and aggregations. For a complete list of supported operations, see the
 :manual:`Operations that Support Collations </reference/collation/#operations-that-support-collation>`
 server manual page.

source/crud/compound-operations.txt

@@ -101,10 +101,10 @@ The output of the preceding code resembles the following:
    {"food": "pizza", "color": "green"}
 
 For more information about the ``Projections`` class, see our
-:doc:`guide on the Projections builder </builders/projections/>`.
+:ref:`guide on the Projections builder <projections-builders>`.
 
 For more information about the upsert operation, see our 
-:doc:`guide on upserts </crud/write-operations/upsert/>`.
+:ref:`guide on upserts <java-upsert>`.
 
 For more information about the methods and classes mentioned in this section,
 see the following API Documentation:
@@ -187,7 +187,7 @@ The output of the preceding code resembles the following:
    {"_id": 2, "food": "pear", "color": "yellow"}
 
 For more information about the ``Sorts`` class, see our
-:doc:`guide on the Sorts builder </builders/sort/>`.
+:ref:`guide on the Sorts builder <sorts-builders>`.
 
 For more information about the methods and classes mentioned in this section,
 see the following API Documentation:
@@ -318,10 +318,10 @@ instance:
    for the duration of your compound operation. 
 
 For information on the ``Updates`` class, see our
-:doc:`guide on the Updates builder </builders/updates/>`.
+:ref:`guide on the Updates builder <updates-builders>`.
 
 For more information of the ``Filters`` class, see our
-:doc:`guide on the Filters builder </builders/filters/>`.
+:ref:`guide on the Filters builder <filters-builders>`.
 
 For more information about the ``findOneAndUpdate()`` method, see 
 the API Documentation for the `MongoCollection class <{+api+}/apidocs/mongodb-driver-sync/com/mongodb/client/MongoCollection.html#findOneAndUpdate(org.bson.conversions.Bson,java.util.List,com.mongodb.client.model.FindOneAndUpdateOptions)>`__.

source/crud/gridfs.txt

@@ -263,8 +263,8 @@ see the following resources:
 
 - `GridFSFindIterable <{+api+}/apidocs/mongodb-driver-sync/com/mongodb/client/gridfs/GridFSFindIterable.html>`__ API Documentation
 - `GridFSBucket.find() <{+api+}/apidocs/mongodb-driver-sync/com/mongodb/client/gridfs/GridFSBucket.html#find(org.bson.conversions.Bson)>`__ API Documentation
-- :doc:`Sort Results </crud/read-operations/sort>`
-- :doc:`Limit the Number of Returned Results </crud/read-operations/limit>`
+- :ref:`Sort Results <java-fundamentals-sort>`
+- :ref:`Limit the Number of Returned Results <java-fundamentals-limit>`
 
 .. _gridfs-download-files:
 

source/crud/query-document.txt

@@ -1,9 +1,9 @@
+.. _java-query:
+
 ===============
 Specify a Query
 ===============
 
-
-
 .. contents:: On this page
    :local:
    :backlinks: none

source/crud/read-operations/geo.txt

@@ -115,7 +115,7 @@ GeoJSON data to a ``2dsphere`` index. The following snippet creates a
    collection.createIndex(Indexes.geo2dsphere("location.geo"));
 
 For more information about the ``Indexes`` builder, see our 
-:doc:`guide on the Indexes builder </builders/indexes>`.
+:ref:`guide on the Indexes builder <indexes-builders>`.
 
 .. guide resource
 
@@ -166,7 +166,7 @@ legacy coordinate pairs to  a ``2d`` index. The following snippet creates a
    collection.createIndex(Indexes.geo2d("coordinates"));
 
 For more information about the ``Indexes`` builder, see our 
-:doc:`guide on the Indexes builder </builders/indexes>`. 
+:ref:`guide on the Indexes builder <indexes-builders>`. 
 
 For more information about legacy coordinate pairs, see the
 :manual:`{+mdb-server+} manual page on legacy coordinate pairs </geospatial-queries/#legacy-coordinate-pairs>`.
@@ -208,7 +208,7 @@ For more information about geospatial query operators, see the
 .. external resource
 
 For more information about ``Filters``, see our 
-:doc:`guide on the Filters builder </builders/filters>`.  
+:ref:`guide on the Filters builder <filters-builders>`.  
 
 Query Parameters
 ~~~~~~~~~~~~~~~~
@@ -229,7 +229,7 @@ Examples
 
 The following examples use the MongoDB Atlas sample dataset. You can learn how
 to  set up your own free-tier Atlas cluster and how to load the sample dataset
-in our :doc:`quick start guide </quick-start>`.
+in our :ref:`quick start guide <java-get-started>`.
 
 The examples use the ``theaters`` collection in the ``sample_mflix`` database
 from the sample dataset. The ``theaters`` collection contains a ``2dsphere`` index
@@ -293,7 +293,7 @@ For more information about the ``$near`` operator, see
 :manual:`the reference documentation for $near </reference/operator/query/near/#mongodb-query-op.-near>`.
 
 For more information about ``Filters``,
-:doc:`see our guide on the Filters builder </builders/filters>`.
+:ref:`see our guide on the Filters builder <filters-builders>`.
 
 Query Within a Range
 ~~~~~~~~~~~~~~~~~~~~

source/crud/read-operations/limit.txt

@@ -25,7 +25,7 @@ to reach the specified limit, it can return a smaller number.
 If you use ``limit()`` with the ``skip()`` instance method, the skip applies
 first and the limit only applies to the documents left over after
 the skip. For more information about the ``skip()`` method, see our
-:doc:`guide on Skipping Returned Documents </crud/read-operations/skip/>`.
+:ref:`guide on Skipping Returned Documents <java-fundamentals-skip>`.
 
 The following examples demonstrate, respectively, how to insert data into
 a collection, how to use ``limit()`` to restrict the number of returned documents,