fix problems

Author: rustagir

source/atlas-vector-search.txt

@@ -63,13 +63,6 @@ The following example shows how to build an aggregation pipeline that uses the
    :language: java
    :dedent:
 
-.. tip:: Query Vector Type
-
-   The preceding example creates an instance of ``BinaryVector`` to
-   serve as the query vector, but you can also create a ``List`` of
-   ``Double`` instances. However, we recommend that you use the
-   ``BinaryVector`` type to improve storage efficiency.
-
 The following example shows how you can run the aggregation and print
 the vector search meta-score from the result of the preceding
 aggregation pipeline:
@@ -103,5 +96,3 @@ guide, see the following API documentation:
 
 - `Projections.metaVectorSearchScore()
   <{+api+}/apidocs/mongodb-driver-core/com/mongodb/client/model/Projections.html#metaVectorSearchScore(java.lang.String)>`__
-
-- `BinaryVector <{+api+}/apidocs/bson/org/bson/BinaryVector.html>`__

source/builders/aggregates.txt

@@ -980,49 +980,3 @@ aggregation stage:
 
 Learn more about this helper from the
 `searchMeta() API documentation <{+api+}/apidocs/mongodb-driver-core/com/mongodb/client/model/Aggregates.html#searchMeta(com.mongodb.client.model.search.SearchCollector)>`__.
-
-.. _java-atlas-vector-search:
-
-Atlas Vector Search
--------------------
-
-.. important::
-
-   To learn what versions of MongoDB Atlas support this feature, see
-   :atlas:`Limitations </atlas-vector-search/vector-search-stage/#limitations>`
-   in the MongoDB Atlas documentation.
-
-Use the ``vectorSearch()`` method to create a :atlas:`$vectorSearch
-</atlas-vector-search/vector-search-stage/>`
-pipeline stage that specifies a **semantic search**. A semantic search is
-a type of search which locates information that is similar in meaning.
-
-To use this feature, you must set up a vector search index and index your
-vector embeddings. To learn about how to programmatically create a
-vector search index, see the :ref:`java-search-indexes` section in the Indexes guide. To
-learn more about vector embeddings, see
-:atlas:`How to Index Vector Embeddings for Vector Search
-</atlas-search/field-types/knn-vector/>`.
-
-The following example shows how to build an aggregation pipeline that uses the
-``vectorSearch()`` and ``project()`` methods to compute a vector search score:
-
-.. literalinclude:: /includes/fundamentals/code-snippets/builders/AggBuilders.java
-   :start-after: // begin vectorSearch
-   :end-before: // end vectorSearch
-   :language: java
-   :dedent:
-
-The following example shows how you can print the score from the result of the
-preceding aggregation pipeline:
-
-.. literalinclude:: /includes/fundamentals/code-snippets/builders/AggBuilders.java
-   :start-after: // begin vectorSearch-output
-   :end-before: // end vectorSearch-output
-   :language: java
-   :dedent:
-
-Learn more about this helper in the
-`vectorSearch()
-<{+api+}/apidocs/mongodb-driver-core/com/mongodb/client/model/Aggregates.html#vectorSearch(com.mongodb.client.model.search.FieldSearchPath,java.lang.Iterable,java.lang.String,long,com.mongodb.client.model.search.VectorSearchOptions)>`__
-API documentation.

source/builders/updates.txt

@@ -1,3 +1,5 @@
+.. _updates-builders:
+
 ================
 Updates Builders
 ================
@@ -8,8 +10,6 @@ Updates Builders
    :depth: 2
    :class: singlecol
 
-.. _updates-builders:
-
 Overview
 --------
 

source/crud/write-operations/modify.txt

@@ -67,7 +67,10 @@ The ``updateOne()`` and ``updateMany()`` methods both have the following
 parameters:
 
 - ``query`` specifies a query filter with the criteria to match documents to update in your collection
-- ``updateDocument`` specifies the fields and values to modify in the matching document or documents. For this example, we use the :doc:`Updates builder </fundamentals/builders/updates>` to create the update document.
+- ``updateDocument`` specifies the fields and values to modify in the
+  matching document or documents. For this example, we use the
+  :ref:`Updates builder <updates-builders>` to create the
+  update document.
 
 You can create the ``updateDocument`` using an ``Updates`` builder as
 follows:

source/databases-collections.txt renamed to source/getting-started/databases-collections.txt

@@ -1,9 +1,9 @@
+.. _java-databases-collections:
+
 =========================
 Databases and Collections
 =========================
 
-.. default-domain:: mongodb
-
 .. contents:: On this page
    :local:
    :backlinks: none

source/index.txt

@@ -21,7 +21,6 @@ MongoDB Java Driver
    Getting Started </getting-started>
    Connect </connection>
    CRUD Operations </crud>
-   Databases and Collations </databases-collections>
    Aggregation </aggregation>
    Builders </builders>
    Data Formats </data-formats>