diff --git a/docs/_layouts/global.html b/docs/_layouts/global.html
index d5fb18bfb0..d05ac6bbe1 100755
--- a/docs/_layouts/global.html
+++ b/docs/_layouts/global.html
@@ -82,7 +82,7 @@
                         <li class="dropdown">
                             <a href="#" class="dropdown-toggle" data-toggle="dropdown">API Docs<b class="caret"></b></a>
                             <ul class="dropdown-menu">
-                                <li><a href="api/scala/index.html#org.apache.spark.package">Scala</a></li>
+                                <li><a href="api/scala/org/apache/spark/index.html">Scala</a></li>
                                 <li><a href="api/java/index.html">Java</a></li>
                                 <li><a href="api/python/index.html">Python</a></li>
                                 <li><a href="api/R/index.html">R</a></li>
diff --git a/docs/configuration.md b/docs/configuration.md
index 1343755f9d..9c9cf84151 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -24,7 +24,7 @@ license: |
 Spark provides three locations to configure the system:
 
 * [Spark properties](#spark-properties) control most application parameters and can be set by using
-  a [SparkConf](api/scala/index.html#org.apache.spark.SparkConf) object, or through Java
+  a [SparkConf](api/scala/org/apache/spark/SparkConf.html) object, or through Java
   system properties.
 * [Environment variables](#environment-variables) can be used to set per-machine settings, such as
   the IP address, through the `conf/spark-env.sh` script on each node.
@@ -34,7 +34,7 @@ Spark provides three locations to configure the system:
 
 Spark properties control most application settings and are configured separately for each
 application. These properties can be set directly on a
-[SparkConf](api/scala/index.html#org.apache.spark.SparkConf) passed to your
+[SparkConf](api/scala/org/apache/spark/SparkConf.html) passed to your
 `SparkContext`. `SparkConf` allows you to configure some of the common properties
 (e.g. master URL and application name), as well as arbitrary key-value pairs through the
 `set()` method. For example, we could initialize an application with two threads as follows:
@@ -1326,7 +1326,7 @@ Apart from these, the following properties are also available, and may be useful
     property is useful if you need to register your classes in a custom way, e.g. to specify a custom
     field serializer. Otherwise <code>spark.kryo.classesToRegister</code> is simpler. It should be
     set to classes that extend
-    <a href="api/scala/index.html#org.apache.spark.serializer.KryoRegistrator">
+    <a href="api/scala/org/apache/spark/serializer/KryoRegistrator.html">
     <code>KryoRegistrator</code></a>.
     See the <a href="tuning.html#data-serialization">tuning guide</a> for more details.
   </td>
@@ -1379,7 +1379,7 @@ Apart from these, the following properties are also available, and may be useful
     but is quite slow, so we recommend <a href="tuning.html">using
     <code>org.apache.spark.serializer.KryoSerializer</code> and configuring Kryo serialization</a>
     when speed is necessary. Can be any subclass of
-    <a href="api/scala/index.html#org.apache.spark.serializer.Serializer">
+    <a href="api/scala/org/apache/spark/serializer/Serializer.html">
     <code>org.apache.spark.Serializer</code></a>.
   </td>
 </tr>
diff --git a/docs/graphx-programming-guide.md b/docs/graphx-programming-guide.md
index 167c44aa1b..50c9366a09 100644
--- a/docs/graphx-programming-guide.md
+++ b/docs/graphx-programming-guide.md
@@ -25,38 +25,38 @@ license: |
 
 <!-- All the documentation links  -->
 
-[EdgeRDD]: api/scala/index.html#org.apache.spark.graphx.EdgeRDD
-[VertexRDD]: api/scala/index.html#org.apache.spark.graphx.VertexRDD
-[Edge]: api/scala/index.html#org.apache.spark.graphx.Edge
-[EdgeTriplet]: api/scala/index.html#org.apache.spark.graphx.EdgeTriplet
-[Graph]: api/scala/index.html#org.apache.spark.graphx.Graph
-[GraphOps]: api/scala/index.html#org.apache.spark.graphx.GraphOps
-[Graph.mapVertices]: api/scala/index.html#org.apache.spark.graphx.Graph@mapVertices[VD2]((VertexId,VD)⇒VD2)(ClassTag[VD2]):Graph[VD2,ED]
-[Graph.reverse]: api/scala/index.html#org.apache.spark.graphx.Graph@reverse:Graph[VD,ED]
-[Graph.subgraph]: api/scala/index.html#org.apache.spark.graphx.Graph@subgraph((EdgeTriplet[VD,ED])⇒Boolean,(VertexId,VD)⇒Boolean):Graph[VD,ED]
-[Graph.mask]: api/scala/index.html#org.apache.spark.graphx.Graph@mask[VD2,ED2](Graph[VD2,ED2])(ClassTag[VD2],ClassTag[ED2]):Graph[VD,ED]
-[Graph.groupEdges]: api/scala/index.html#org.apache.spark.graphx.Graph@groupEdges((ED,ED)⇒ED):Graph[VD,ED]
-[GraphOps.joinVertices]: api/scala/index.html#org.apache.spark.graphx.GraphOps@joinVertices[U](RDD[(VertexId,U)])((VertexId,VD,U)⇒VD)(ClassTag[U]):Graph[VD,ED]
-[Graph.outerJoinVertices]: api/scala/index.html#org.apache.spark.graphx.Graph@outerJoinVertices[U,VD2](RDD[(VertexId,U)])((VertexId,VD,Option[U])⇒VD2)(ClassTag[U],ClassTag[VD2]):Graph[VD2,ED]
-[Graph.aggregateMessages]: api/scala/index.html#org.apache.spark.graphx.Graph@aggregateMessages[A]((EdgeContext[VD,ED,A])⇒Unit,(A,A)⇒A,TripletFields)(ClassTag[A]):VertexRDD[A]
-[EdgeContext]: api/scala/index.html#org.apache.spark.graphx.EdgeContext
-[GraphOps.collectNeighborIds]: api/scala/index.html#org.apache.spark.graphx.GraphOps@collectNeighborIds(EdgeDirection):VertexRDD[Array[VertexId]]
-[GraphOps.collectNeighbors]: api/scala/index.html#org.apache.spark.graphx.GraphOps@collectNeighbors(EdgeDirection):VertexRDD[Array[(VertexId,VD)]]
+[EdgeRDD]: api/scala/org/apache/spark/graphx/EdgeRDD.html
+[VertexRDD]: api/scala/org/apache/spark/graphx/VertexRDD.html
+[Edge]: api/scala/org/apache/spark/graphx/Edge.html
+[EdgeTriplet]: api/scala/org/apache/spark/graphx/EdgeTriplet.html
+[Graph]: api/scala/org/apache/spark/graphx/Graph$.html
+[GraphOps]: api/scala/org/apache/spark/graphx/GraphOps.html
+[Graph.mapVertices]: api/scala/org/apache/spark/graphx/Graph.html#mapVertices[VD2]((VertexId,VD)⇒VD2)(ClassTag[VD2]):Graph[VD2,ED]
+[Graph.reverse]: api/scala/org/apache/spark/graphx/Graph.html#reverse:Graph[VD,ED]
+[Graph.subgraph]: api/scala/org/apache/spark/graphx/Graph.html#subgraph((EdgeTriplet[VD,ED])⇒Boolean,(VertexId,VD)⇒Boolean):Graph[VD,ED]
+[Graph.mask]: api/scala/org/apache/spark/graphx/Graph.html#mask[VD2,ED2](Graph[VD2,ED2])(ClassTag[VD2],ClassTag[ED2]):Graph[VD,ED]
+[Graph.groupEdges]: api/scala/org/apache/spark/graphx/Graph.html#groupEdges((ED,ED)⇒ED):Graph[VD,ED]
+[GraphOps.joinVertices]: api/scala/org/apache/spark/graphx/GraphOps.html#joinVertices[U](RDD[(VertexId,U)])((VertexId,VD,U)⇒VD)(ClassTag[U]):Graph[VD,ED]
+[Graph.outerJoinVertices]: api/scala/org/apache/spark/graphx/Graph.html#outerJoinVertices[U,VD2](RDD[(VertexId,U)])((VertexId,VD,Option[U])⇒VD2)(ClassTag[U],ClassTag[VD2]):Graph[VD2,ED]
+[Graph.aggregateMessages]: api/scala/org/apache/spark/graphx/Graph.html#aggregateMessages[A]((EdgeContext[VD,ED,A])⇒Unit,(A,A)⇒A,TripletFields)(ClassTag[A]):VertexRDD[A]
+[EdgeContext]: api/scala/org/apache/spark/graphx/EdgeContext.html
+[GraphOps.collectNeighborIds]: api/scala/org/apache/spark/graphx/GraphOps.html#collectNeighborIds(EdgeDirection):VertexRDD[Array[VertexId]]
+[GraphOps.collectNeighbors]: api/scala/org/apache/spark/graphx/GraphOps.html#collectNeighbors(EdgeDirection):VertexRDD[Array[(VertexId,VD)]]
 [RDD Persistence]: rdd-programming-guide.html#rdd-persistence
-[Graph.cache]: api/scala/index.html#org.apache.spark.graphx.Graph@cache():Graph[VD,ED]
-[GraphOps.pregel]: api/scala/index.html#org.apache.spark.graphx.GraphOps@pregel[A](A,Int,EdgeDirection)((VertexId,VD,A)⇒VD,(EdgeTriplet[VD,ED])⇒Iterator[(VertexId,A)],(A,A)⇒A)(ClassTag[A]):Graph[VD,ED]
-[PartitionStrategy]: api/scala/index.html#org.apache.spark.graphx.PartitionStrategy$
-[GraphLoader.edgeListFile]: api/scala/index.html#org.apache.spark.graphx.GraphLoader$@edgeListFile(SparkContext,String,Boolean,Int):Graph[Int,Int]
-[Graph.apply]: api/scala/index.html#org.apache.spark.graphx.Graph$@apply[VD,ED](RDD[(VertexId,VD)],RDD[Edge[ED]],VD)(ClassTag[VD],ClassTag[ED]):Graph[VD,ED]
-[Graph.fromEdgeTuples]: api/scala/index.html#org.apache.spark.graphx.Graph$@fromEdgeTuples[VD](RDD[(VertexId,VertexId)],VD,Option[PartitionStrategy])(ClassTag[VD]):Graph[VD,Int]
-[Graph.fromEdges]: api/scala/index.html#org.apache.spark.graphx.Graph$@fromEdges[VD,ED](RDD[Edge[ED]],VD)(ClassTag[VD],ClassTag[ED]):Graph[VD,ED]
-[PartitionStrategy]: api/scala/index.html#org.apache.spark.graphx.PartitionStrategy
-[PageRank]: api/scala/index.html#org.apache.spark.graphx.lib.PageRank$
-[ConnectedComponents]: api/scala/index.html#org.apache.spark.graphx.lib.ConnectedComponents$
-[TriangleCount]: api/scala/index.html#org.apache.spark.graphx.lib.TriangleCount$
-[Graph.partitionBy]: api/scala/index.html#org.apache.spark.graphx.Graph@partitionBy(PartitionStrategy):Graph[VD,ED]
-[EdgeContext.sendToSrc]: api/scala/index.html#org.apache.spark.graphx.EdgeContext@sendToSrc(msg:A):Unit
-[EdgeContext.sendToDst]: api/scala/index.html#org.apache.spark.graphx.EdgeContext@sendToDst(msg:A):Unit
+[Graph.cache]: api/scala/org/apache/spark/graphx/Graph.html#cache():Graph[VD,ED]
+[GraphOps.pregel]: api/scala/org/apache/spark/graphx/GraphOps.html#pregel[A](A,Int,EdgeDirection)((VertexId,VD,A)⇒VD,(EdgeTriplet[VD,ED])⇒Iterator[(VertexId,A)],(A,A)⇒A)(ClassTag[A]):Graph[VD,ED]
+[PartitionStrategy]: api/scala/org/apache/spark/graphx/PartitionStrategy$.html
+[GraphLoader.edgeListFile]: api/scala/org/apache/spark/graphx/GraphLoader$.html#edgeListFile(SparkContext,String,Boolean,Int):Graph[Int,Int]
+[Graph.apply]: api/scala/org/apache/spark/graphx/Graph$.html#apply[VD,ED](RDD[(VertexId,VD)],RDD[Edge[ED]],VD)(ClassTag[VD],ClassTag[ED]):Graph[VD,ED]
+[Graph.fromEdgeTuples]: api/scala/org/apache/spark/graphx/Graph$.html#fromEdgeTuples[VD](RDD[(VertexId,VertexId)],VD,Option[PartitionStrategy])(ClassTag[VD]):Graph[VD,Int]
+[Graph.fromEdges]: api/scala/org/apache/spark/graphx/Graph$.html#fromEdges[VD,ED](RDD[Edge[ED]],VD)(ClassTag[VD],ClassTag[ED]):Graph[VD,ED]
+[PartitionStrategy]: api/scala/org/apache/spark/graphx/PartitionStrategy$.html
+[PageRank]: api/scala/org/apache/spark/graphx/lib/PageRank$.html
+[ConnectedComponents]: api/scala/org/apache/spark/graphx/lib/ConnectedComponents$.html
+[TriangleCount]: api/scala/org/apache/spark/graphx/lib/TriangleCount$.html
+[Graph.partitionBy]: api/scala/org/apache/spark/graphx/Graph.html#partitionBy(PartitionStrategy):Graph[VD,ED]
+[EdgeContext.sendToSrc]: api/scala/org/apache/spark/graphx/EdgeContext.html#sendToSrc(msg:A):Unit
+[EdgeContext.sendToDst]: api/scala/org/apache/spark/graphx/EdgeContext.html#sendToDst(msg:A):Unit
 [TripletFields]: api/java/org/apache/spark/graphx/TripletFields.html
 [TripletFields.All]: api/java/org/apache/spark/graphx/TripletFields.html#All
 [TripletFields.None]: api/java/org/apache/spark/graphx/TripletFields.html#None
@@ -74,7 +74,7 @@ license: |
 # Overview
 
 GraphX is a new component in Spark for graphs and graph-parallel computation. At a high level,
-GraphX extends the Spark [RDD](api/scala/index.html#org.apache.spark.rdd.RDD) by introducing a
+GraphX extends the Spark [RDD](api/scala/org/apache/spark/rdd/RDD.html) by introducing a
 new [Graph](#property_graph) abstraction: a directed multigraph with properties
 attached to each vertex and edge.  To support graph computation, GraphX exposes a set of fundamental
 operators (e.g., [subgraph](#structural_operators), [joinVertices](#join_operators), and
@@ -99,7 +99,7 @@ getting started with Spark refer to the [Spark Quick Start Guide](quick-start.ht
 
 # The Property Graph
 
-The [property graph](api/scala/index.html#org.apache.spark.graphx.Graph) is a directed multigraph
+The [property graph](api/scala/org/apache/spark/graphx/Graph.html) is a directed multigraph
 with user defined objects attached to each vertex and edge.  A directed multigraph is a directed
 graph with potentially multiple parallel edges sharing the same source and destination vertex.  The
 ability to support parallel edges simplifies modeling scenarios where there can be multiple
@@ -175,7 +175,7 @@ val userGraph: Graph[(String, String), String]
 There are numerous ways to construct a property graph from raw files, RDDs, and even synthetic
 generators and these are discussed in more detail in the section on
 [graph builders](#graph_builders).  Probably the most general method is to use the
-[Graph object](api/scala/index.html#org.apache.spark.graphx.Graph$).  For example the following
+[Graph object](api/scala/org/apache/spark/graphx/Graph$.html).  For example the following
 code constructs a graph from a collection of RDDs:
 
 {% highlight scala %}
diff --git a/docs/index.md b/docs/index.md
index f6ec595231..38f12dd4db 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -118,7 +118,7 @@ options for deployment:
 
 **API Docs:**
 
-* [Spark Scala API (Scaladoc)](api/scala/index.html#org.apache.spark.package)
+* [Spark Scala API (Scaladoc)](api/scala/org/apache/spark/index.html)
 * [Spark Java API (Javadoc)](api/java/index.html)
 * [Spark Python API (Sphinx)](api/python/index.html)
 * [Spark R API (Roxygen2)](api/R/index.html)
diff --git a/docs/ml-advanced.md b/docs/ml-advanced.md
index 5787fe914c..0e19bca92d 100644
--- a/docs/ml-advanced.md
+++ b/docs/ml-advanced.md
@@ -55,10 +55,10 @@ other first-order optimizations.
 Quasi-Newton](https://www.microsoft.com/en-us/research/wp-content/uploads/2007/01/andrew07scalable.pdf)
 (OWL-QN) is an extension of L-BFGS that can effectively handle L1 and elastic net regularization.
 
-L-BFGS is used as a solver for [LinearRegression](api/scala/index.html#org.apache.spark.ml.regression.LinearRegression),
-[LogisticRegression](api/scala/index.html#org.apache.spark.ml.classification.LogisticRegression),
-[AFTSurvivalRegression](api/scala/index.html#org.apache.spark.ml.regression.AFTSurvivalRegression)
-and [MultilayerPerceptronClassifier](api/scala/index.html#org.apache.spark.ml.classification.MultilayerPerceptronClassifier).
+L-BFGS is used as a solver for [LinearRegression](api/scala/org/apache/spark/ml/regression/LinearRegression.html),
+[LogisticRegression](api/scala/org/apache/spark/ml/classification/LogisticRegression.html),
+[AFTSurvivalRegression](api/scala/org/apache/spark/ml/regression/AFTSurvivalRegression.html)
+and [MultilayerPerceptronClassifier](api/scala/org/apache/spark/ml/classification/MultilayerPerceptronClassifier.html).
 
 MLlib L-BFGS solver calls the corresponding implementation in [breeze](https://github.com/scalanlp/breeze/blob/master/math/src/main/scala/breeze/optimize/LBFGS.scala).
 
@@ -108,4 +108,4 @@ It solves certain optimization problems iteratively through the following proced
 
 Since it involves solving a weighted least squares (WLS) problem by `WeightedLeastSquares` in each iteration,
 it also requires the number of features to be no more than 4096.
-Currently IRLS is used as the default solver of [GeneralizedLinearRegression](api/scala/index.html#org.apache.spark.ml.regression.GeneralizedLinearRegression).
+Currently IRLS is used as the default solver of [GeneralizedLinearRegression](api/scala/org/apache/spark/ml/regression/GeneralizedLinearRegression.html).
diff --git a/docs/ml-classification-regression.md b/docs/ml-classification-regression.md
index 630a15d853..9d5388005e 100644
--- a/docs/ml-classification-regression.md
+++ b/docs/ml-classification-regression.md
@@ -71,7 +71,7 @@ $\alpha$ and `regParam` corresponds to $\lambda$.
 
 <div data-lang="scala" markdown="1">
 
-More details on parameters can be found in the [Scala API documentation](api/scala/index.html#org.apache.spark.ml.classification.LogisticRegression).
+More details on parameters can be found in the [Scala API documentation](api/scala/org/apache/spark/ml/classification/LogisticRegression.html).
 
 {% include_example scala/org/apache/spark/examples/ml/LogisticRegressionWithElasticNetExample.scala %}
 </div>
@@ -109,12 +109,12 @@ only available on the driver.
 
 <div data-lang="scala" markdown="1">
 
-[`LogisticRegressionTrainingSummary`](api/scala/index.html#org.apache.spark.ml.classification.LogisticRegressionTrainingSummary)
+[`LogisticRegressionTrainingSummary`](api/scala/org/apache/spark/ml/classification/LogisticRegressionTrainingSummary.html)
 provides a summary for a
-[`LogisticRegressionModel`](api/scala/index.html#org.apache.spark.ml.classification.LogisticRegressionModel).
+[`LogisticRegressionModel`](api/scala/org/apache/spark/ml/classification/LogisticRegressionModel.html).
 In the case of binary classification, certain additional metrics are
 available, e.g. ROC curve. The binary summary can be accessed via the
-`binarySummary` method. See [`BinaryLogisticRegressionTrainingSummary`](api/scala/index.html#org.apache.spark.ml.classification.BinaryLogisticRegressionTrainingSummary).
+`binarySummary` method. See [`BinaryLogisticRegressionTrainingSummary`](api/scala/org/apache/spark/ml/classification/BinaryLogisticRegressionTrainingSummary.html).
 
 Continuing the earlier example:
 
@@ -216,7 +216,7 @@ We use two feature transformers to prepare the data; these help index categories
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-More details on parameters can be found in the [Scala API documentation](api/scala/index.html#org.apache.spark.ml.classification.DecisionTreeClassifier).
+More details on parameters can be found in the [Scala API documentation](api/scala/org/apache/spark/ml/classification/DecisionTreeClassifier.html).
 
 {% include_example scala/org/apache/spark/examples/ml/DecisionTreeClassificationExample.scala %}
 
@@ -261,7 +261,7 @@ We use two feature transformers to prepare the data; these help index categories
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.RandomForestClassifier) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/RandomForestClassifier.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/RandomForestClassifierExample.scala %}
 </div>
@@ -302,7 +302,7 @@ We use two feature transformers to prepare the data; these help index categories
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.GBTClassifier) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/GBTClassifier.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/GradientBoostedTreeClassifierExample.scala %}
 </div>
@@ -358,7 +358,7 @@ MLPC employs backpropagation for learning the model. We use the logistic loss fu
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.MultilayerPerceptronClassifier) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/MultilayerPerceptronClassifier.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/MultilayerPerceptronClassifierExample.scala %}
 </div>
@@ -403,7 +403,7 @@ in Spark ML supports binary classification with linear SVM. Internally, it optim
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.LinearSVC) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/LinearSVC.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/LinearSVCExample.scala %}
 </div>
@@ -447,7 +447,7 @@ The example below demonstrates how to load the
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.OneVsRest) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/OneVsRest.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/OneVsRestExample.scala %}
 </div>
@@ -501,7 +501,7 @@ setting the parameter $\lambda$ (default to $1.0$).
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.NaiveBayes) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/NaiveBayes.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/NaiveBayesExample.scala %}
 </div>
@@ -544,7 +544,7 @@ We scale features to be between 0 and 1 to prevent the exploding gradient proble
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.classification.FMClassifier) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/classification/FMClassifier.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/FMClassifierExample.scala %}
 </div>
@@ -585,7 +585,7 @@ regression model and extracting model summary statistics.
 
 <div data-lang="scala" markdown="1">
 
-More details on parameters can be found in the [Scala API documentation](api/scala/index.html#org.apache.spark.ml.regression.LinearRegression).
+More details on parameters can be found in the [Scala API documentation](api/scala/org/apache/spark/ml/regression/LinearRegression.html).
 
 {% include_example scala/org/apache/spark/examples/ml/LinearRegressionWithElasticNetExample.scala %}
 </div>
@@ -726,7 +726,7 @@ function and extracting model summary statistics.
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.regression.GeneralizedLinearRegression) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/regression/GeneralizedLinearRegression.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/GeneralizedLinearRegressionExample.scala %}
 </div>
@@ -768,7 +768,7 @@ We use a feature transformer to index categorical features, adding metadata to t
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-More details on parameters can be found in the [Scala API documentation](api/scala/index.html#org.apache.spark.ml.regression.DecisionTreeRegressor).
+More details on parameters can be found in the [Scala API documentation](api/scala/org/apache/spark/ml/regression/DecisionTreeRegressor.html).
 
 {% include_example scala/org/apache/spark/examples/ml/DecisionTreeRegressionExample.scala %}
 </div>
@@ -810,7 +810,7 @@ We use a feature transformer to index categorical features, adding metadata to t
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.regression.RandomForestRegressor) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/regression/RandomForestRegressor.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/RandomForestRegressorExample.scala %}
 </div>
@@ -851,7 +851,7 @@ be true in general.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.regression.GBTRegressor) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/regression/GBTRegressor.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/GradientBoostedTreeRegressorExample.scala %}
 </div>
@@ -945,7 +945,7 @@ The implementation matches the result from R's survival function
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.regression.AFTSurvivalRegression) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/regression/AFTSurvivalRegression.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala %}
 </div>
@@ -1025,7 +1025,7 @@ is treated as piecewise linear function. The rules for prediction therefore are:
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [`IsotonicRegression` Scala docs](api/scala/index.html#org.apache.spark.ml.regression.IsotonicRegression) for details on the API.
+Refer to the [`IsotonicRegression` Scala docs](api/scala/org/apache/spark/ml/regression/IsotonicRegression.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/IsotonicRegressionExample.scala %}
 </div>
@@ -1066,7 +1066,7 @@ We scale features to be between 0 and 1 to prevent the exploding gradient proble
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.regression.FMRegressor) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/regression/FMRegressor.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/FMRegressorExample.scala %}
 </div>
diff --git a/docs/ml-clustering.md b/docs/ml-clustering.md
index 2775d0421c..4574567fa9 100644
--- a/docs/ml-clustering.md
+++ b/docs/ml-clustering.md
@@ -85,7 +85,7 @@ called [kmeans||](http://theory.stanford.edu/~sergei/papers/vldb12-kmpar.pdf).
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.clustering.KMeans) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/clustering/KMeans.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/KMeansExample.scala %}
 </div>
@@ -123,7 +123,7 @@ and generates a `LDAModel` as the base model. Expert users may cast a `LDAModel`
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.clustering.LDA) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/clustering/LDA.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/LDAExample.scala %}
 </div>
@@ -166,7 +166,7 @@ Bisecting K-means can often be much faster than regular K-means, but it will gen
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.clustering.BisectingKMeans) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/clustering/BisectingKMeans.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/BisectingKMeansExample.scala %}
 </div>
@@ -255,7 +255,7 @@ model.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.clustering.GaussianMixture) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/clustering/GaussianMixture.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/GaussianMixtureExample.scala %}
 </div>
@@ -302,7 +302,7 @@ using truncated power iteration on a normalized pair-wise similarity matrix of t
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.clustering.PowerIterationClustering) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/clustering/PowerIterationClustering.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/PowerIterationClusteringExample.scala %}
 </div>
diff --git a/docs/ml-collaborative-filtering.md b/docs/ml-collaborative-filtering.md
index e6e596bed1..6c41efd5cc 100644
--- a/docs/ml-collaborative-filtering.md
+++ b/docs/ml-collaborative-filtering.md
@@ -115,7 +115,7 @@ explicit (`implicitPrefs` is `false`).
 We evaluate the recommendation model by measuring the root-mean-square error of
 rating prediction.
 
-Refer to the [`ALS` Scala docs](api/scala/index.html#org.apache.spark.ml.recommendation.ALS)
+Refer to the [`ALS` Scala docs](api/scala/org/apache/spark/ml/recommendation/ALS.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ALSExample.scala %}
diff --git a/docs/ml-datasource.md b/docs/ml-datasource.md
index 5dc2d057a9..0f2f5f482e 100644
--- a/docs/ml-datasource.md
+++ b/docs/ml-datasource.md
@@ -42,7 +42,7 @@ The schema of the `image` column is:
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`ImageDataSource`](api/scala/index.html#org.apache.spark.ml.source.image.ImageDataSource)
+[`ImageDataSource`](api/scala/org/apache/spark/ml/source/image/ImageDataSource.html)
 implements a Spark SQL data source API for loading image data as a DataFrame.
 
 {% highlight scala %}
@@ -133,7 +133,7 @@ The schemas of the columns are:
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`LibSVMDataSource`](api/scala/index.html#org.apache.spark.ml.source.libsvm.LibSVMDataSource)
+[`LibSVMDataSource`](api/scala/org/apache/spark/ml/source/libsvm/LibSVMDataSource.html)
 implements a Spark SQL data source API for loading `LIBSVM` data as a DataFrame.
 
 {% highlight scala %}
diff --git a/docs/ml-features.md b/docs/ml-features.md
index 92d2f3d0b4..9c05fd5fa1 100644
--- a/docs/ml-features.md
+++ b/docs/ml-features.md
@@ -96,8 +96,8 @@ when using text as features.  Our feature vectors could then be passed to a lear
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [HashingTF Scala docs](api/scala/index.html#org.apache.spark.ml.feature.HashingTF) and
-the [IDF Scala docs](api/scala/index.html#org.apache.spark.ml.feature.IDF) for more details on the API.
+Refer to the [HashingTF Scala docs](api/scala/org/apache/spark/ml/feature/HashingTF.html) and
+the [IDF Scala docs](api/scala/org/apache/spark/ml/feature/IDF.html) for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/TfIdfExample.scala %}
 </div>
@@ -135,7 +135,7 @@ In the following code segment, we start with a set of documents, each of which i
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Word2Vec Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Word2Vec)
+Refer to the [Word2Vec Scala docs](api/scala/org/apache/spark/ml/feature/Word2Vec.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/Word2VecExample.scala %}
@@ -200,8 +200,8 @@ Each vector represents the token counts of the document over the vocabulary.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [CountVectorizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.CountVectorizer)
-and the [CountVectorizerModel Scala docs](api/scala/index.html#org.apache.spark.ml.feature.CountVectorizerModel)
+Refer to the [CountVectorizer Scala docs](api/scala/org/apache/spark/ml/feature/CountVectorizer.html)
+and the [CountVectorizerModel Scala docs](api/scala/org/apache/spark/ml/feature/CountVectorizerModel.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/CountVectorizerExample.scala %}
@@ -286,7 +286,7 @@ The resulting feature vectors could then be passed to a learning algorithm.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [FeatureHasher Scala docs](api/scala/index.html#org.apache.spark.ml.feature.FeatureHasher)
+Refer to the [FeatureHasher Scala docs](api/scala/org/apache/spark/ml/feature/FeatureHasher.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/FeatureHasherExample.scala %}
@@ -313,9 +313,9 @@ for more details on the API.
 
 ## Tokenizer
 
-[Tokenization](http://en.wikipedia.org/wiki/Lexical_analysis#Tokenization) is the process of taking text (such as a sentence) and breaking it into individual terms (usually words).  A simple [Tokenizer](api/scala/index.html#org.apache.spark.ml.feature.Tokenizer) class provides this functionality.  The example below shows how to split sentences into sequences of words.
+[Tokenization](http://en.wikipedia.org/wiki/Lexical_analysis#Tokenization) is the process of taking text (such as a sentence) and breaking it into individual terms (usually words).  A simple [Tokenizer](api/scala/org/apache/spark/ml/feature/Tokenizer.html) class provides this functionality.  The example below shows how to split sentences into sequences of words.
 
-[RegexTokenizer](api/scala/index.html#org.apache.spark.ml.feature.RegexTokenizer) allows more
+[RegexTokenizer](api/scala/org/apache/spark/ml/feature/RegexTokenizer.html) allows more
  advanced tokenization based on regular expression (regex) matching.
  By default, the parameter "pattern" (regex, default: `"\\s+"`) is used as delimiters to split the input text.
  Alternatively, users can set parameter "gaps" to false indicating the regex "pattern" denotes
@@ -326,8 +326,8 @@ for more details on the API.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Tokenizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Tokenizer)
-and the [RegexTokenizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.RegexTokenizer)
+Refer to the [Tokenizer Scala docs](api/scala/org/apache/spark/ml/feature/Tokenizer.html)
+and the [RegexTokenizer Scala docs](api/scala/org/apache/spark/ml/feature/RegexTokenizer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/TokenizerExample.scala %}
@@ -395,7 +395,7 @@ filtered out.
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [StopWordsRemover Scala docs](api/scala/index.html#org.apache.spark.ml.feature.StopWordsRemover)
+Refer to the [StopWordsRemover Scala docs](api/scala/org/apache/spark/ml/feature/StopWordsRemover.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/StopWordsRemoverExample.scala %}
@@ -430,7 +430,7 @@ An [n-gram](https://en.wikipedia.org/wiki/N-gram) is a sequence of $n$ tokens (t
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [NGram Scala docs](api/scala/index.html#org.apache.spark.ml.feature.NGram)
+Refer to the [NGram Scala docs](api/scala/org/apache/spark/ml/feature/NGram.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/NGramExample.scala %}
@@ -468,7 +468,7 @@ for `inputCol`.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Binarizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Binarizer)
+Refer to the [Binarizer Scala docs](api/scala/org/apache/spark/ml/feature/Binarizer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/BinarizerExample.scala %}
@@ -493,14 +493,14 @@ for more details on the API.
 
 ## PCA
 
-[PCA](http://en.wikipedia.org/wiki/Principal_component_analysis) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. A [PCA](api/scala/index.html#org.apache.spark.ml.feature.PCA) class trains a model to project vectors to a low-dimensional space using PCA. The example below shows how to project 5-dimensional feature vectors into 3-dimensional principal components.
+[PCA](http://en.wikipedia.org/wiki/Principal_component_analysis) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. A [PCA](api/scala/org/apache/spark/ml/feature/PCA.html) class trains a model to project vectors to a low-dimensional space using PCA. The example below shows how to project 5-dimensional feature vectors into 3-dimensional principal components.
 
 **Examples**
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [PCA Scala docs](api/scala/index.html#org.apache.spark.ml.feature.PCA)
+Refer to the [PCA Scala docs](api/scala/org/apache/spark/ml/feature/PCA.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/PCAExample.scala %}
@@ -525,14 +525,14 @@ for more details on the API.
 
 ## PolynomialExpansion
 
-[Polynomial expansion](http://en.wikipedia.org/wiki/Polynomial_expansion) is the process of expanding your features into a polynomial space, which is formulated by an n-degree combination of original dimensions. A [PolynomialExpansion](api/scala/index.html#org.apache.spark.ml.feature.PolynomialExpansion) class provides this functionality.  The example below shows how to expand your features into a 3-degree polynomial space.
+[Polynomial expansion](http://en.wikipedia.org/wiki/Polynomial_expansion) is the process of expanding your features into a polynomial space, which is formulated by an n-degree combination of original dimensions. A [PolynomialExpansion](api/scala/org/apache/spark/ml/feature/PolynomialExpansion.html) class provides this functionality.  The example below shows how to expand your features into a 3-degree polynomial space.
 
 **Examples**
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [PolynomialExpansion Scala docs](api/scala/index.html#org.apache.spark.ml.feature.PolynomialExpansion)
+Refer to the [PolynomialExpansion Scala docs](api/scala/org/apache/spark/ml/feature/PolynomialExpansion.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/PolynomialExpansionExample.scala %}
@@ -561,7 +561,7 @@ The [Discrete Cosine
 Transform](https://en.wikipedia.org/wiki/Discrete_cosine_transform)
 transforms a length $N$ real-valued sequence in the time domain into
 another length $N$ real-valued sequence in the frequency domain. A
-[DCT](api/scala/index.html#org.apache.spark.ml.feature.DCT) class
+[DCT](api/scala/org/apache/spark/ml/feature/DCT.html) class
 provides this functionality, implementing the
 [DCT-II](https://en.wikipedia.org/wiki/Discrete_cosine_transform#DCT-II)
 and scaling the result by $1/\sqrt{2}$ such that the representing matrix
@@ -574,7 +574,7 @@ $0$th DCT coefficient and _not_ the $N/2$th).
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [DCT Scala docs](api/scala/index.html#org.apache.spark.ml.feature.DCT)
+Refer to the [DCT Scala docs](api/scala/org/apache/spark/ml/feature/DCT.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/DCTExample.scala %}
@@ -704,7 +704,7 @@ Notice that the rows containing "d" or "e" are mapped to index "3.0"
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [StringIndexer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.StringIndexer)
+Refer to the [StringIndexer Scala docs](api/scala/org/apache/spark/ml/feature/StringIndexer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/StringIndexerExample.scala %}
@@ -770,7 +770,7 @@ labels (they will be inferred from the columns' metadata):
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [IndexToString Scala docs](api/scala/index.html#org.apache.spark.ml.feature.IndexToString)
+Refer to the [IndexToString Scala docs](api/scala/org/apache/spark/ml/feature/IndexToString.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/IndexToStringExample.scala %}
@@ -809,7 +809,7 @@ for more details on the API.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [OneHotEncoder Scala docs](api/scala/index.html#org.apache.spark.ml.feature.OneHotEncoder) for more details on the API.
+Refer to the [OneHotEncoder Scala docs](api/scala/org/apache/spark/ml/feature/OneHotEncoder.html) for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/OneHotEncoderExample.scala %}
 </div>
@@ -835,7 +835,7 @@ Refer to the [OneHotEncoder Python docs](api/python/pyspark.ml.html#pyspark.ml.f
 `VectorIndexer` helps index categorical features in datasets of `Vector`s.
 It can both automatically decide which features are categorical and convert original values to category indices.  Specifically, it does the following:
 
-1. Take an input column of type [Vector](api/scala/index.html#org.apache.spark.ml.linalg.Vector) and a parameter `maxCategories`.
+1. Take an input column of type [Vector](api/scala/org/apache/spark/ml/linalg/Vector.html) and a parameter `maxCategories`.
 2. Decide which features should be categorical based on the number of distinct values, where features with at most `maxCategories` are declared categorical.
 3. Compute 0-based category indices for each categorical feature.
 4. Index categorical features and transform original feature values to indices.
@@ -849,7 +849,7 @@ In the example below, we read in a dataset of labeled points and then use `Vecto
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [VectorIndexer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.VectorIndexer)
+Refer to the [VectorIndexer Scala docs](api/scala/org/apache/spark/ml/feature/VectorIndexer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/VectorIndexerExample.scala %}
@@ -910,7 +910,7 @@ then `interactedCol` as the output column contains:
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Interaction Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Interaction)
+Refer to the [Interaction Scala docs](api/scala/org/apache/spark/ml/feature/Interaction.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/InteractionExample.scala %}
@@ -944,7 +944,7 @@ The following example demonstrates how to load a dataset in libsvm format and th
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Normalizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Normalizer)
+Refer to the [Normalizer Scala docs](api/scala/org/apache/spark/ml/feature/Normalizer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/NormalizerExample.scala %}
@@ -986,7 +986,7 @@ The following example demonstrates how to load a dataset in libsvm format and th
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [StandardScaler Scala docs](api/scala/index.html#org.apache.spark.ml.feature.StandardScaler)
+Refer to the [StandardScaler Scala docs](api/scala/org/apache/spark/ml/feature/StandardScaler.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/StandardScalerExample.scala %}
@@ -1030,7 +1030,7 @@ The following example demonstrates how to load a dataset in libsvm format and th
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [RobustScaler Scala docs](api/scala/index.html#org.apache.spark.ml.feature.RobustScaler)
+Refer to the [RobustScaler Scala docs](api/scala/org/apache/spark/ml/feature/RobustScaler.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/RobustScalerExample.scala %}
@@ -1078,8 +1078,8 @@ The following example demonstrates how to load a dataset in libsvm format and th
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [MinMaxScaler Scala docs](api/scala/index.html#org.apache.spark.ml.feature.MinMaxScaler)
-and the [MinMaxScalerModel Scala docs](api/scala/index.html#org.apache.spark.ml.feature.MinMaxScalerModel)
+Refer to the [MinMaxScaler Scala docs](api/scala/org/apache/spark/ml/feature/MinMaxScaler.html)
+and the [MinMaxScalerModel Scala docs](api/scala/org/apache/spark/ml/feature/MinMaxScalerModel.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/MinMaxScalerExample.scala %}
@@ -1121,8 +1121,8 @@ The following example demonstrates how to load a dataset in libsvm format and th
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [MaxAbsScaler Scala docs](api/scala/index.html#org.apache.spark.ml.feature.MaxAbsScaler)
-and the [MaxAbsScalerModel Scala docs](api/scala/index.html#org.apache.spark.ml.feature.MaxAbsScalerModel)
+Refer to the [MaxAbsScaler Scala docs](api/scala/org/apache/spark/ml/feature/MaxAbsScaler.html)
+and the [MaxAbsScalerModel Scala docs](api/scala/org/apache/spark/ml/feature/MaxAbsScalerModel.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/MaxAbsScalerExample.scala %}
@@ -1157,7 +1157,7 @@ Note that if you have no idea of the upper and lower bounds of the targeted colu
 
 Note also that the splits that you provided have to be in strictly increasing order, i.e. `s0 < s1 < s2 < ... < sn`.
 
-More details can be found in the API docs for [Bucketizer](api/scala/index.html#org.apache.spark.ml.feature.Bucketizer).
+More details can be found in the API docs for [Bucketizer](api/scala/org/apache/spark/ml/feature/Bucketizer.html).
 
 **Examples**
 
@@ -1166,7 +1166,7 @@ The following example demonstrates how to bucketize a column of `Double`s into a
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Bucketizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Bucketizer)
+Refer to the [Bucketizer Scala docs](api/scala/org/apache/spark/ml/feature/Bucketizer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/BucketizerExample.scala %}
@@ -1216,7 +1216,7 @@ This example below demonstrates how to transform vectors using a transforming ve
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [ElementwiseProduct Scala docs](api/scala/index.html#org.apache.spark.ml.feature.ElementwiseProduct)
+Refer to the [ElementwiseProduct Scala docs](api/scala/org/apache/spark/ml/feature/ElementwiseProduct.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ElementwiseProductExample.scala %}
@@ -1276,7 +1276,7 @@ This is the output of the `SQLTransformer` with statement `"SELECT *, (v1 + v2)
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [SQLTransformer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.SQLTransformer)
+Refer to the [SQLTransformer Scala docs](api/scala/org/apache/spark/ml/feature/SQLTransformer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/SQLTransformerExample.scala %}
@@ -1336,7 +1336,7 @@ output column to `features`, after transformation we should get the following Da
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [VectorAssembler Scala docs](api/scala/index.html#org.apache.spark.ml.feature.VectorAssembler)
+Refer to the [VectorAssembler Scala docs](api/scala/org/apache/spark/ml/feature/VectorAssembler.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/VectorAssemblerExample.scala %}
@@ -1387,7 +1387,7 @@ to avoid this kind of inconsistent state.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [VectorSizeHint Scala docs](api/scala/index.html#org.apache.spark.ml.feature.VectorSizeHint)
+Refer to the [VectorSizeHint Scala docs](api/scala/org/apache/spark/ml/feature/VectorSizeHint.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/VectorSizeHintExample.scala %}
@@ -1426,7 +1426,7 @@ NaN values, they will be handled specially and placed into their own bucket, for
 are used, then non-NaN data will be put into buckets[0-3], but NaNs will be counted in a special bucket[4].
 
 Algorithm: The bin ranges are chosen using an approximate algorithm (see the documentation for
-[approxQuantile](api/scala/index.html#org.apache.spark.sql.DataFrameStatFunctions) for a
+[approxQuantile](api/scala/org/apache/spark/sql/DataFrameStatFunctions.html) for a
 detailed description). The precision of the approximation can be controlled with the
 `relativeError` parameter. When set to zero, exact quantiles are calculated
 (**Note:** Computing exact quantiles is an expensive operation). The lower and upper bin bounds
@@ -1470,7 +1470,7 @@ a categorical one. Given `numBuckets = 3`, we should get the following DataFrame
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [QuantileDiscretizer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.QuantileDiscretizer)
+Refer to the [QuantileDiscretizer Scala docs](api/scala/org/apache/spark/ml/feature/QuantileDiscretizer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/QuantileDiscretizerExample.scala %}
@@ -1539,7 +1539,7 @@ the relevant column.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [Imputer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.Imputer)
+Refer to the [Imputer Scala docs](api/scala/org/apache/spark/ml/feature/Imputer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ImputerExample.scala %}
@@ -1620,7 +1620,7 @@ Suppose also that we have potential input attributes for the `userFeatures`, i.e
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [VectorSlicer Scala docs](api/scala/index.html#org.apache.spark.ml.feature.VectorSlicer)
+Refer to the [VectorSlicer Scala docs](api/scala/org/apache/spark/ml/feature/VectorSlicer.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/VectorSlicerExample.scala %}
@@ -1706,7 +1706,7 @@ id | country | hour | clicked | features         | label
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [RFormula Scala docs](api/scala/index.html#org.apache.spark.ml.feature.RFormula)
+Refer to the [RFormula Scala docs](api/scala/org/apache/spark/ml/feature/RFormula.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/RFormulaExample.scala %}
@@ -1770,7 +1770,7 @@ id | features              | clicked | selectedFeatures
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [ChiSqSelector Scala docs](api/scala/index.html#org.apache.spark.ml.feature.ChiSqSelector)
+Refer to the [ChiSqSelector Scala docs](api/scala/org/apache/spark/ml/feature/ChiSqSelector.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ChiSqSelectorExample.scala %}
@@ -1856,7 +1856,7 @@ Bucketed Random Projection accepts arbitrary vectors as input features, and supp
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [BucketedRandomProjectionLSH Scala docs](api/scala/index.html#org.apache.spark.ml.feature.BucketedRandomProjectionLSH)
+Refer to the [BucketedRandomProjectionLSH Scala docs](api/scala/org/apache/spark/ml/feature/BucketedRandomProjectionLSH.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/BucketedRandomProjectionLSHExample.scala %}
@@ -1897,7 +1897,7 @@ The input sets for MinHash are represented as binary vectors, where the vector i
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [MinHashLSH Scala docs](api/scala/index.html#org.apache.spark.ml.feature.MinHashLSH)
+Refer to the [MinHashLSH Scala docs](api/scala/org/apache/spark/ml/feature/MinHashLSH.html)
 for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/MinHashLSHExample.scala %}
diff --git a/docs/ml-frequent-pattern-mining.md b/docs/ml-frequent-pattern-mining.md
index a243188603..42d7e50357 100644
--- a/docs/ml-frequent-pattern-mining.md
+++ b/docs/ml-frequent-pattern-mining.md
@@ -75,7 +75,7 @@ The `FPGrowthModel` provides:
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.fpm.FPGrowth) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/fpm/FPGrowth.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/FPGrowthExample.scala %}
 </div>
@@ -128,7 +128,7 @@ pattern mining problem.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [Scala API docs](api/scala/index.html#org.apache.spark.ml.fpm.PrefixSpan) for more details.
+Refer to the [Scala API docs](api/scala/org/apache/spark/ml/fpm/PrefixSpan.html) for more details.
 
 {% include_example scala/org/apache/spark/examples/ml/PrefixSpanExample.scala %}
 </div>
diff --git a/docs/ml-migration-guide.md b/docs/ml-migration-guide.md
index 860c941e6b..f3cd762b6f 100644
--- a/docs/ml-migration-guide.md
+++ b/docs/ml-migration-guide.md
@@ -187,7 +187,7 @@ val mlVec: org.apache.spark.ml.linalg.Vector = mllibVec.asML
 val mlMat: org.apache.spark.ml.linalg.Matrix = mllibMat.asML
 {% endhighlight %}
 
-Refer to the [`MLUtils` Scala docs](api/scala/index.html#org.apache.spark.mllib.util.MLUtils$) for further detail.
+Refer to the [`MLUtils` Scala docs](api/scala/org/apache/spark/mllib/util/MLUtils$.html) for further detail.
 </div>
 
 <div data-lang="java" markdown="1">
@@ -341,9 +341,9 @@ In the `spark.ml` package, there exists one breaking API change and one behavior
 In the `spark.mllib` package, there were several breaking changes, but all in `DeveloperApi` or `Experimental` APIs:
 
 * Gradient-Boosted Trees
-    * *(Breaking change)* The signature of the [`Loss.gradient`](api/scala/index.html#org.apache.spark.mllib.tree.loss.Loss) method was changed.  This is only an issues for users who wrote their own losses for GBTs.
-    * *(Breaking change)* The `apply` and `copy` methods for the case class [`BoostingStrategy`](api/scala/index.html#org.apache.spark.mllib.tree.configuration.BoostingStrategy) have been changed because of a modification to the case class fields.  This could be an issue for users who use `BoostingStrategy` to set GBT parameters.
-* *(Breaking change)* The return value of [`LDA.run`](api/scala/index.html#org.apache.spark.mllib.clustering.LDA) has changed.  It now returns an abstract class `LDAModel` instead of the concrete class `DistributedLDAModel`.  The object of type `LDAModel` can still be cast to the appropriate concrete type, which depends on the optimization algorithm.
+    * *(Breaking change)* The signature of the [`Loss.gradient`](api/scala/org/apache/spark/mllib/tree/loss/Loss.html) method was changed.  This is only an issues for users who wrote their own losses for GBTs.
+    * *(Breaking change)* The `apply` and `copy` methods for the case class [`BoostingStrategy`](api/scala/org/apache/spark/mllib/tree/configuration/BoostingStrategy.html) have been changed because of a modification to the case class fields.  This could be an issue for users who use `BoostingStrategy` to set GBT parameters.
+* *(Breaking change)* The return value of [`LDA.run`](api/scala/org/apache/spark/mllib/clustering/LDA.html) has changed.  It now returns an abstract class `LDAModel` instead of the concrete class `DistributedLDAModel`.  The object of type `LDAModel` can still be cast to the appropriate concrete type, which depends on the optimization algorithm.
 
 In the `spark.ml` package, several major API changes occurred, including:
 
@@ -359,12 +359,12 @@ changes for future releases.
 
 In the `spark.mllib` package, there were several breaking changes.  The first change (in `ALS`) is the only one in a component not marked as Alpha or Experimental.
 
-* *(Breaking change)* In [`ALS`](api/scala/index.html#org.apache.spark.mllib.recommendation.ALS), the extraneous method `solveLeastSquares` has been removed.  The `DeveloperApi` method `analyzeBlocks` was also removed.
-* *(Breaking change)* [`StandardScalerModel`](api/scala/index.html#org.apache.spark.mllib.feature.StandardScalerModel) remains an Alpha component. In it, the `variance` method has been replaced with the `std` method.  To compute the column variance values returned by the original `variance` method, simply square the standard deviation values returned by `std`.
-* *(Breaking change)* [`StreamingLinearRegressionWithSGD`](api/scala/index.html#org.apache.spark.mllib.regression.StreamingLinearRegressionWithSGD) remains an Experimental component.  In it, there were two changes:
+* *(Breaking change)* In [`ALS`](api/scala/org/apache/spark/mllib/recommendation/ALS.html), the extraneous method `solveLeastSquares` has been removed.  The `DeveloperApi` method `analyzeBlocks` was also removed.
+* *(Breaking change)* [`StandardScalerModel`](api/scala/org/apache/spark/mllib/feature/StandardScalerModel.html) remains an Alpha component. In it, the `variance` method has been replaced with the `std` method.  To compute the column variance values returned by the original `variance` method, simply square the standard deviation values returned by `std`.
+* *(Breaking change)* [`StreamingLinearRegressionWithSGD`](api/scala/org/apache/spark/mllib/regression/StreamingLinearRegressionWithSGD.html) remains an Experimental component.  In it, there were two changes:
     * The constructor taking arguments was removed in favor of a builder pattern using the default constructor plus parameter setter methods.
     * Variable `model` is no longer public.
-* *(Breaking change)* [`DecisionTree`](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree) remains an Experimental component.  In it and its associated classes, there were several changes:
+* *(Breaking change)* [`DecisionTree`](api/scala/org/apache/spark/mllib/tree/DecisionTree.html) remains an Experimental component.  In it and its associated classes, there were several changes:
     * In `DecisionTree`, the deprecated class method `train` has been removed.  (The object/static `train` methods remain.)
     * In `Strategy`, the `checkpointDir` parameter has been removed.  Checkpointing is still supported, but the checkpoint directory must be set before calling tree and tree ensemble training.
 * `PythonMLlibAPI` (the interface between Scala/Java and Python for MLlib) was a public API but is now private, declared `private[python]`.  This was never meant for external use.
@@ -373,31 +373,31 @@ In the `spark.mllib` package, there were several breaking changes.  The first ch
 
 In the `spark.ml` package, the main API changes are from Spark SQL.  We list the most important changes here:
 
-* The old [SchemaRDD](https://spark.apache.org/docs/1.2.1/api/scala/index.html#org.apache.spark.sql.SchemaRDD) has been replaced with [DataFrame](api/scala/index.html#org.apache.spark.sql.DataFrame) with a somewhat modified API.  All algorithms in `spark.ml` which used to use SchemaRDD now use DataFrame.
+* The old [SchemaRDD](https://spark.apache.org/docs/1.2.1/api/scala/index.html#org.apache.spark.sql.SchemaRDD) has been replaced with [DataFrame](api/scala/org/apache/spark/sql/DataFrame.html) with a somewhat modified API.  All algorithms in `spark.ml` which used to use SchemaRDD now use DataFrame.
 * In Spark 1.2, we used implicit conversions from `RDD`s of `LabeledPoint` into `SchemaRDD`s by calling `import sqlContext._` where `sqlContext` was an instance of `SQLContext`.  These implicits have been moved, so we now call `import sqlContext.implicits._`.
 * Java APIs for SQL have also changed accordingly.  Please see the examples above and the [Spark SQL Programming Guide](sql-programming-guide.html) for details.
 
 Other changes were in `LogisticRegression`:
 
 * The `scoreCol` output column (with default value "score") was renamed to be `probabilityCol` (with default value "probability").  The type was originally `Double` (for the probability of class 1.0), but it is now `Vector` (for the probability of each class, to support multiclass classification in the future).
-* In Spark 1.2, `LogisticRegressionModel` did not include an intercept.  In Spark 1.3, it includes an intercept; however, it will always be 0.0 since it uses the default settings for [spark.mllib.LogisticRegressionWithLBFGS](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithLBFGS).  The option to use an intercept will be added in the future.
+* In Spark 1.2, `LogisticRegressionModel` did not include an intercept.  In Spark 1.3, it includes an intercept; however, it will always be 0.0 since it uses the default settings for [spark.mllib.LogisticRegressionWithLBFGS](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithLBFGS.html).  The option to use an intercept will be added in the future.
 
 ## Upgrading from MLlib 1.1 to 1.2
 
 The only API changes in MLlib v1.2 are in
-[`DecisionTree`](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree),
+[`DecisionTree`](api/scala/org/apache/spark/mllib/tree/DecisionTree.html),
 which continues to be an experimental API in MLlib 1.2:
 
 1. *(Breaking change)* The Scala API for classification takes a named argument specifying the number
 of classes.  In MLlib v1.1, this argument was called `numClasses` in Python and
 `numClassesForClassification` in Scala.  In MLlib v1.2, the names are both set to `numClasses`.
 This `numClasses` parameter is specified either via
-[`Strategy`](api/scala/index.html#org.apache.spark.mllib.tree.configuration.Strategy)
-or via [`DecisionTree`](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree)
+[`Strategy`](api/scala/org/apache/spark/mllib/tree/configuration/Strategy.html)
+or via [`DecisionTree`](api/scala/org/apache/spark/mllib/tree/DecisionTree.html)
 static `trainClassifier` and `trainRegressor` methods.
 
 2. *(Breaking change)* The API for
-[`Node`](api/scala/index.html#org.apache.spark.mllib.tree.model.Node) has changed.
+[`Node`](api/scala/org/apache/spark/mllib/tree/model/Node.html) has changed.
 This should generally not affect user code, unless the user manually constructs decision trees
 (instead of using the `trainClassifier` or `trainRegressor` methods).
 The tree `Node` now includes more information, including the probability of the predicted label
@@ -411,7 +411,7 @@ Examples in the Spark distribution and examples in the
 ## Upgrading from MLlib 1.0 to 1.1
 
 The only API changes in MLlib v1.1 are in
-[`DecisionTree`](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree),
+[`DecisionTree`](api/scala/org/apache/spark/mllib/tree/DecisionTree.html),
 which continues to be an experimental API in MLlib 1.1:
 
 1. *(Breaking change)* The meaning of tree depth has been changed by 1 in order to match
@@ -421,12 +421,12 @@ and in [rpart](http://cran.r-project.org/web/packages/rpart/index.html).
 In MLlib v1.0, a depth-1 tree had 1 leaf node, and a depth-2 tree had 1 root node and 2 leaf nodes.
 In MLlib v1.1, a depth-0 tree has 1 leaf node, and a depth-1 tree has 1 root node and 2 leaf nodes.
 This depth is specified by the `maxDepth` parameter in
-[`Strategy`](api/scala/index.html#org.apache.spark.mllib.tree.configuration.Strategy)
-or via [`DecisionTree`](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree)
+[`Strategy`](api/scala/org/apache/spark/mllib/tree/configuration/Strategy.html)
+or via [`DecisionTree`](api/scala/org/apache/spark/mllib/tree/DecisionTree.html)
 static `trainClassifier` and `trainRegressor` methods.
 
 2. *(Non-breaking change)* We recommend using the newly added `trainClassifier` and `trainRegressor`
-methods to build a [`DecisionTree`](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree),
+methods to build a [`DecisionTree`](api/scala/org/apache/spark/mllib/tree/DecisionTree.html),
 rather than using the old parameter class `Strategy`.  These new training methods explicitly
 separate classification and regression, and they replace specialized parameter types with
 simple `String` types.
diff --git a/docs/ml-pipeline.md b/docs/ml-pipeline.md
index 993a428ab5..0b581e1a09 100644
--- a/docs/ml-pipeline.md
+++ b/docs/ml-pipeline.md
@@ -238,7 +238,7 @@ notes, then it should be treated as a bug to be fixed.
 
 This section gives code examples illustrating the functionality discussed above.
 For more info, please refer to the API documentation
-([Scala](api/scala/index.html#org.apache.spark.ml.package),
+([Scala](api/scala/org/apache/spark/ml/package.html),
 [Java](api/java/org/apache/spark/ml/package-summary.html),
 and [Python](api/python/pyspark.ml.html)).
 
@@ -250,9 +250,9 @@ This example covers the concepts of `Estimator`, `Transformer`, and `Param`.
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [`Estimator` Scala docs](api/scala/index.html#org.apache.spark.ml.Estimator),
-the [`Transformer` Scala docs](api/scala/index.html#org.apache.spark.ml.Transformer) and
-the [`Params` Scala docs](api/scala/index.html#org.apache.spark.ml.param.Params) for details on the API.
+Refer to the [`Estimator` Scala docs](api/scala/org/apache/spark/ml/Estimator.html),
+the [`Transformer` Scala docs](api/scala/org/apache/spark/ml/Transformer.html) and
+the [`Params` Scala docs](api/scala/org/apache/spark/ml/param/Params.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/EstimatorTransformerParamExample.scala %}
 </div>
@@ -285,7 +285,7 @@ This example follows the simple text document `Pipeline` illustrated in the figu
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [`Pipeline` Scala docs](api/scala/index.html#org.apache.spark.ml.Pipeline) for details on the API.
+Refer to the [`Pipeline` Scala docs](api/scala/org/apache/spark/ml/Pipeline.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/PipelineExample.scala %}
 </div>
diff --git a/docs/ml-statistics.md b/docs/ml-statistics.md
index 997c57244b..a3d57ff7d2 100644
--- a/docs/ml-statistics.md
+++ b/docs/ml-statistics.md
@@ -50,7 +50,7 @@ correlation methods are currently Pearson's and Spearman's correlation.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`Correlation`](api/scala/index.html#org.apache.spark.ml.stat.Correlation$)
+[`Correlation`](api/scala/org/apache/spark/ml/stat/Correlation$.html)
 computes the correlation matrix for the input Dataset of Vectors using the specified method.
 The output will be a DataFrame that contains the correlation matrix of the column of vectors.
 
@@ -87,7 +87,7 @@ the Chi-squared statistic is computed. All label and feature values must be cate
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`ChiSquareTest` Scala docs](api/scala/index.html#org.apache.spark.ml.stat.ChiSquareTest$) for details on the API.
+Refer to the [`ChiSquareTest` Scala docs](api/scala/org/apache/spark/ml/stat/ChiSquareTest$.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ChiSquareTestExample.scala %}
 </div>
@@ -114,7 +114,7 @@ as well as the total count.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-The following example demonstrates using [`Summarizer`](api/scala/index.html#org.apache.spark.ml.stat.Summarizer$)
+The following example demonstrates using [`Summarizer`](api/scala/org/apache/spark/ml/stat/Summarizer$.html)
 to compute the mean and variance for a vector column of the input dataframe, with and without a weight column.
 
 {% include_example scala/org/apache/spark/examples/ml/SummarizerExample.scala %}
@@ -133,4 +133,4 @@ Refer to the [`Summarizer` Python docs](api/python/index.html#pyspark.ml.stat.Su
 {% include_example python/ml/summarizer_example.py %}
 </div>
 
-</div>
\ No newline at end of file
+</div>
diff --git a/docs/ml-tuning.md b/docs/ml-tuning.md
index 0717cce538..49e23684e5 100644
--- a/docs/ml-tuning.md
+++ b/docs/ml-tuning.md
@@ -49,12 +49,12 @@ Built-in Cross-Validation and other tooling allow users to optimize hyperparamet
 An important task in ML is *model selection*, or using data to find the best model or parameters for a given task.  This is also called *tuning*.
 Tuning may be done for individual `Estimator`s such as `LogisticRegression`, or for entire `Pipeline`s which include multiple algorithms, featurization, and other steps.  Users can tune an entire `Pipeline` at once, rather than tuning each element in the `Pipeline` separately.
 
-MLlib supports model selection using tools such as [`CrossValidator`](api/scala/index.html#org.apache.spark.ml.tuning.CrossValidator) and [`TrainValidationSplit`](api/scala/index.html#org.apache.spark.ml.tuning.TrainValidationSplit).
+MLlib supports model selection using tools such as [`CrossValidator`](api/scala/org/apache/spark/ml/tuning/CrossValidator.html) and [`TrainValidationSplit`](api/scala/org/apache/spark/ml/tuning/TrainValidationSplit.html).
 These tools require the following items:
 
-* [`Estimator`](api/scala/index.html#org.apache.spark.ml.Estimator): algorithm or `Pipeline` to tune
+* [`Estimator`](api/scala/org/apache/spark/ml/Estimator.html): algorithm or `Pipeline` to tune
 * Set of `ParamMap`s: parameters to choose from, sometimes called a "parameter grid" to search over
-* [`Evaluator`](api/scala/index.html#org.apache.spark.ml.evaluation.Evaluator): metric to measure how well a fitted `Model` does on held-out test data
+* [`Evaluator`](api/scala/org/apache/spark/ml/evaluation/Evaluator.html): metric to measure how well a fitted `Model` does on held-out test data
 
 At a high level, these model selection tools work as follows:
 
@@ -63,13 +63,13 @@ At a high level, these model selection tools work as follows:
   * For each `ParamMap`, they fit the `Estimator` using those parameters, get the fitted `Model`, and evaluate the `Model`'s performance using the `Evaluator`.
 * They select the `Model` produced by the best-performing set of parameters.
 
-The `Evaluator` can be a [`RegressionEvaluator`](api/scala/index.html#org.apache.spark.ml.evaluation.RegressionEvaluator)
-for regression problems, a [`BinaryClassificationEvaluator`](api/scala/index.html#org.apache.spark.ml.evaluation.BinaryClassificationEvaluator)
-for binary data, or a [`MulticlassClassificationEvaluator`](api/scala/index.html#org.apache.spark.ml.evaluation.MulticlassClassificationEvaluator)
+The `Evaluator` can be a [`RegressionEvaluator`](api/scala/org/apache/spark/ml/evaluation/RegressionEvaluator.html)
+for regression problems, a [`BinaryClassificationEvaluator`](api/scala/org/apache/spark/ml/evaluation/BinaryClassificationEvaluator.html)
+for binary data, or a [`MulticlassClassificationEvaluator`](api/scala/org/apache/spark/ml/evaluation/MulticlassClassificationEvaluator.html)
 for multiclass problems. The default metric used to choose the best `ParamMap` can be overridden by the `setMetricName`
 method in each of these evaluators.
 
-To help construct the parameter grid, users can use the [`ParamGridBuilder`](api/scala/index.html#org.apache.spark.ml.tuning.ParamGridBuilder) utility.
+To help construct the parameter grid, users can use the [`ParamGridBuilder`](api/scala/org/apache/spark/ml/tuning/ParamGridBuilder.html) utility.
 By default, sets of parameters from the parameter grid are evaluated in serial. Parameter evaluation can be done in parallel by setting `parallelism` with a value of 2 or more (a value of 1 will be serial) before running model selection with `CrossValidator` or `TrainValidationSplit`.
 The value of `parallelism` should be chosen carefully to maximize parallelism without exceeding cluster resources, and larger values may not always lead to improved performance.  Generally speaking, a value up to 10 should be sufficient for most clusters.
 
@@ -93,7 +93,7 @@ However, it is also a well-established method for choosing parameters which is m
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [`CrossValidator` Scala docs](api/scala/index.html#org.apache.spark.ml.tuning.CrossValidator) for details on the API.
+Refer to the [`CrossValidator` Scala docs](api/scala/org/apache/spark/ml/tuning/CrossValidator.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ModelSelectionViaCrossValidationExample.scala %}
 </div>
@@ -133,7 +133,7 @@ Like `CrossValidator`, `TrainValidationSplit` finally fits the `Estimator` using
 
 <div data-lang="scala" markdown="1">
 
-Refer to the [`TrainValidationSplit` Scala docs](api/scala/index.html#org.apache.spark.ml.tuning.TrainValidationSplit) for details on the API.
+Refer to the [`TrainValidationSplit` Scala docs](api/scala/org/apache/spark/ml/tuning/TrainValidationSplit.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/ml/ModelSelectionViaTrainValidationSplitExample.scala %}
 </div>
diff --git a/docs/mllib-clustering.md b/docs/mllib-clustering.md
index 12c33a5e38..4cb2e259cc 100644
--- a/docs/mllib-clustering.md
+++ b/docs/mllib-clustering.md
@@ -55,12 +55,12 @@ initialization via k-means\|\|.
 The following code snippets can be executed in `spark-shell`.
 
 In the following example after loading and parsing data, we use the
-[`KMeans`](api/scala/index.html#org.apache.spark.mllib.clustering.KMeans) object to cluster the data
+[`KMeans`](api/scala/org/apache/spark/mllib/clustering/KMeans.html) object to cluster the data
 into two clusters. The number of desired clusters is passed to the algorithm. We then compute Within
 Set Sum of Squared Error (WSSSE). You can reduce this error measure by increasing *k*. In fact, the
 optimal *k* is usually one where there is an "elbow" in the WSSSE graph.
 
-Refer to the [`KMeans` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.KMeans) and [`KMeansModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.KMeansModel) for details on the API.
+Refer to the [`KMeans` Scala docs](api/scala/org/apache/spark/mllib/clustering/KMeans.html) and [`KMeansModel` Scala docs](api/scala/org/apache/spark/mllib/clustering/KMeansModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/KMeansExample.scala %}
 </div>
@@ -111,11 +111,11 @@ has the following parameters:
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 In the following example after loading and parsing data, we use a
-[GaussianMixture](api/scala/index.html#org.apache.spark.mllib.clustering.GaussianMixture)
+[GaussianMixture](api/scala/org/apache/spark/mllib/clustering/GaussianMixture.html)
 object to cluster the data into two clusters. The number of desired clusters is passed
 to the algorithm. We then output the parameters of the mixture model.
 
-Refer to the [`GaussianMixture` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.GaussianMixture) and [`GaussianMixtureModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.GaussianMixtureModel) for details on the API.
+Refer to the [`GaussianMixture` Scala docs](api/scala/org/apache/spark/mllib/clustering/GaussianMixture.html) and [`GaussianMixtureModel` Scala docs](api/scala/org/apache/spark/mllib/clustering/GaussianMixtureModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/GaussianMixtureExample.scala %}
 </div>
@@ -172,15 +172,15 @@ In the following, we show code snippets to demonstrate how to use PIC in `spark.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-[`PowerIterationClustering`](api/scala/index.html#org.apache.spark.mllib.clustering.PowerIterationClustering) 
+[`PowerIterationClustering`](api/scala/org/apache/spark/mllib/clustering/PowerIterationClustering.html) 
 implements the PIC algorithm.
 It takes an `RDD` of `(srcId: Long, dstId: Long, similarity: Double)` tuples representing the
 affinity matrix.
 Calling `PowerIterationClustering.run` returns a
-[`PowerIterationClusteringModel`](api/scala/index.html#org.apache.spark.mllib.clustering.PowerIterationClusteringModel),
+[`PowerIterationClusteringModel`](api/scala/org/apache/spark/mllib/clustering/PowerIterationClusteringModel.html),
 which contains the computed clustering assignments.
 
-Refer to the [`PowerIterationClustering` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.PowerIterationClustering) and [`PowerIterationClusteringModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.PowerIterationClusteringModel) for details on the API.
+Refer to the [`PowerIterationClustering` Scala docs](api/scala/org/apache/spark/mllib/clustering/PowerIterationClustering.html) and [`PowerIterationClusteringModel` Scala docs](api/scala/org/apache/spark/mllib/clustering/PowerIterationClusteringModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala %}
 </div>
@@ -278,9 +278,9 @@ separately.
 **Expectation Maximization**
 
 Implemented in
-[`EMLDAOptimizer`](api/scala/index.html#org.apache.spark.mllib.clustering.EMLDAOptimizer)
+[`EMLDAOptimizer`](api/scala/org/apache/spark/mllib/clustering/EMLDAOptimizer.html)
 and
-[`DistributedLDAModel`](api/scala/index.html#org.apache.spark.mllib.clustering.DistributedLDAModel).
+[`DistributedLDAModel`](api/scala/org/apache/spark/mllib/clustering/DistributedLDAModel.html).
 
 For the parameters provided to `LDA`:
 
@@ -350,13 +350,13 @@ perplexity of the provided `documents` given the inferred topics.
 **Examples**
 
 In the following example, we load word count vectors representing a corpus of documents.
-We then use [LDA](api/scala/index.html#org.apache.spark.mllib.clustering.LDA)
+We then use [LDA](api/scala/org/apache/spark/mllib/clustering/LDA.html)
 to infer three topics from the documents. The number of desired clusters is passed
 to the algorithm. We then output the topics, represented as probability distributions over words.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`LDA` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.LDA) and [`DistributedLDAModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.DistributedLDAModel) for details on the API.
+Refer to the [`LDA` Scala docs](api/scala/org/apache/spark/mllib/clustering/LDA.html) and [`DistributedLDAModel` Scala docs](api/scala/org/apache/spark/mllib/clustering/DistributedLDAModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/LatentDirichletAllocationExample.scala %}
 </div>
@@ -398,7 +398,7 @@ The implementation in MLlib has the following parameters:
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`BisectingKMeans` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.BisectingKMeans) and [`BisectingKMeansModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.BisectingKMeansModel) for details on the API.
+Refer to the [`BisectingKMeans` Scala docs](api/scala/org/apache/spark/mllib/clustering/BisectingKMeans.html) and [`BisectingKMeansModel` Scala docs](api/scala/org/apache/spark/mllib/clustering/BisectingKMeansModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/BisectingKMeansExample.scala %}
 </div>
@@ -451,7 +451,7 @@ This example shows how to estimate clusters on streaming data.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`StreamingKMeans` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.StreamingKMeans) for details on the API.
+Refer to the [`StreamingKMeans` Scala docs](api/scala/org/apache/spark/mllib/clustering/StreamingKMeans.html) for details on the API.
 And Refer to [Spark Streaming Programming Guide](streaming-programming-guide.html#initializing) for details on StreamingContext.
 
 {% include_example scala/org/apache/spark/examples/mllib/StreamingKMeansExample.scala %}
diff --git a/docs/mllib-collaborative-filtering.md b/docs/mllib-collaborative-filtering.md
index 21546a6326..aaefa59c4a 100644
--- a/docs/mllib-collaborative-filtering.md
+++ b/docs/mllib-collaborative-filtering.md
@@ -76,11 +76,11 @@ best parameter learned from a sampled subset to the full dataset and expect simi
 
 <div data-lang="scala" markdown="1">
 In the following example, we load rating data. Each row consists of a user, a product and a rating.
-We use the default [ALS.train()](api/scala/index.html#org.apache.spark.mllib.recommendation.ALS$) 
+We use the default [ALS.train()](api/scala/org/apache/spark/mllib/recommendation/ALS$.html)
 method which assumes ratings are explicit. We evaluate the
 recommendation model by measuring the Mean Squared Error of rating prediction.
 
-Refer to the [`ALS` Scala docs](api/scala/index.html#org.apache.spark.mllib.recommendation.ALS) for more details on the API.
+Refer to the [`ALS` Scala docs](api/scala/org/apache/spark/mllib/recommendation/ALS.html) for more details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/RecommendationExample.scala %}
 
diff --git a/docs/mllib-data-types.md b/docs/mllib-data-types.md
index cdac46284b..6d3b1a599d 100644
--- a/docs/mllib-data-types.md
+++ b/docs/mllib-data-types.md
@@ -42,13 +42,13 @@ of the vector.
 <div data-lang="scala" markdown="1">
 
 The base class of local vectors is
-[`Vector`](api/scala/index.html#org.apache.spark.mllib.linalg.Vector), and we provide two
-implementations: [`DenseVector`](api/scala/index.html#org.apache.spark.mllib.linalg.DenseVector) and
-[`SparseVector`](api/scala/index.html#org.apache.spark.mllib.linalg.SparseVector).  We recommend
+[`Vector`](api/scala/org/apache/spark/mllib/linalg/Vector.html), and we provide two
+implementations: [`DenseVector`](api/scala/org/apache/spark/mllib/linalg/DenseVector.html) and
+[`SparseVector`](api/scala/org/apache/spark/mllib/linalg/SparseVector.html).  We recommend
 using the factory methods implemented in
-[`Vectors`](api/scala/index.html#org.apache.spark.mllib.linalg.Vectors$) to create local vectors.
+[`Vectors`](api/scala/org/apache/spark/mllib/linalg/Vectors$.html) to create local vectors.
 
-Refer to the [`Vector` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.Vector) and [`Vectors` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.Vectors$) for details on the API.
+Refer to the [`Vector` Scala docs](api/scala/org/apache/spark/mllib/linalg/Vector.html) and [`Vectors` Scala docs](api/scala/org/apache/spark/mllib/linalg/Vectors$.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.{Vector, Vectors}
@@ -138,9 +138,9 @@ For multiclass classification, labels should be class indices starting from zero
 <div data-lang="scala" markdown="1">
 
 A labeled point is represented by the case class
-[`LabeledPoint`](api/scala/index.html#org.apache.spark.mllib.regression.LabeledPoint).
+[`LabeledPoint`](api/scala/org/apache/spark/mllib/regression/LabeledPoint.html).
 
-Refer to the [`LabeledPoint` Scala docs](api/scala/index.html#org.apache.spark.mllib.regression.LabeledPoint) for details on the API.
+Refer to the [`LabeledPoint` Scala docs](api/scala/org/apache/spark/mllib/regression/LabeledPoint.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.Vectors
@@ -211,10 +211,10 @@ After loading, the feature indices are converted to zero-based.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-[`MLUtils.loadLibSVMFile`](api/scala/index.html#org.apache.spark.mllib.util.MLUtils$) reads training
+[`MLUtils.loadLibSVMFile`](api/scala/org/apache/spark/mllib/util/MLUtils$.html) reads training
 examples stored in LIBSVM format.
 
-Refer to the [`MLUtils` Scala docs](api/scala/index.html#org.apache.spark.mllib.util.MLUtils$) for details on the API.
+Refer to the [`MLUtils` Scala docs](api/scala/org/apache/spark/mllib/util/MLUtils$.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.regression.LabeledPoint
@@ -272,14 +272,14 @@ is stored in a one-dimensional array `[1.0, 3.0, 5.0, 2.0, 4.0, 6.0]` with the m
 <div data-lang="scala" markdown="1">
 
 The base class of local matrices is
-[`Matrix`](api/scala/index.html#org.apache.spark.mllib.linalg.Matrix), and we provide two
-implementations: [`DenseMatrix`](api/scala/index.html#org.apache.spark.mllib.linalg.DenseMatrix),
-and [`SparseMatrix`](api/scala/index.html#org.apache.spark.mllib.linalg.SparseMatrix).
+[`Matrix`](api/scala/org/apache/spark/mllib/linalg/Matrix.html), and we provide two
+implementations: [`DenseMatrix`](api/scala/org/apache/spark/mllib/linalg/DenseMatrix.html),
+and [`SparseMatrix`](api/scala/org/apache/spark/mllib/linalg/SparseMatrix.html).
 We recommend using the factory methods implemented
-in [`Matrices`](api/scala/index.html#org.apache.spark.mllib.linalg.Matrices$) to create local
+in [`Matrices`](api/scala/org/apache/spark/mllib/linalg/Matrices$.html) to create local
 matrices. Remember, local matrices in MLlib are stored in column-major order.
 
-Refer to the [`Matrix` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.Matrix) and [`Matrices` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.Matrices$) for details on the API.
+Refer to the [`Matrix` Scala docs](api/scala/org/apache/spark/mllib/linalg/Matrix.html) and [`Matrices` Scala docs](api/scala/org/apache/spark/mllib/linalg/Matrices$.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.{Matrix, Matrices}
@@ -377,12 +377,12 @@ limited by the integer range but it should be much smaller in practice.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-A [`RowMatrix`](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.RowMatrix) can be
+A [`RowMatrix`](api/scala/org/apache/spark/mllib/linalg/distributed/RowMatrix.html) can be
 created from an `RDD[Vector]` instance.  Then we can compute its column summary statistics and decompositions.
 [QR decomposition](https://en.wikipedia.org/wiki/QR_decomposition) is of the form A = QR where Q is an orthogonal matrix and R is an upper triangular matrix.
 For [singular value decomposition (SVD)](https://en.wikipedia.org/wiki/Singular_value_decomposition) and [principal component analysis (PCA)](https://en.wikipedia.org/wiki/Principal_component_analysis), please refer to [Dimensionality reduction](mllib-dimensionality-reduction.html).
 
-Refer to the [`RowMatrix` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.RowMatrix) for details on the API.
+Refer to the [`RowMatrix` Scala docs](api/scala/org/apache/spark/mllib/linalg/distributed/RowMatrix.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.Vector
@@ -463,13 +463,13 @@ vector.
 <div data-lang="scala" markdown="1">
 
 An
-[`IndexedRowMatrix`](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.IndexedRowMatrix)
+[`IndexedRowMatrix`](api/scala/org/apache/spark/mllib/linalg/distributed/IndexedRowMatrix.html)
 can be created from an `RDD[IndexedRow]` instance, where
-[`IndexedRow`](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.IndexedRow) is a
+[`IndexedRow`](api/scala/org/apache/spark/mllib/linalg/distributed/IndexedRow.html) is a
 wrapper over `(Long, Vector)`.  An `IndexedRowMatrix` can be converted to a `RowMatrix` by dropping
 its row indices.
 
-Refer to the [`IndexedRowMatrix` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.IndexedRowMatrix) for details on the API.
+Refer to the [`IndexedRowMatrix` Scala docs](api/scala/org/apache/spark/mllib/linalg/distributed/IndexedRowMatrix.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.distributed.{IndexedRow, IndexedRowMatrix, RowMatrix}
@@ -568,14 +568,14 @@ dimensions of the matrix are huge and the matrix is very sparse.
 <div data-lang="scala" markdown="1">
 
 A
-[`CoordinateMatrix`](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.CoordinateMatrix)
+[`CoordinateMatrix`](api/scala/org/apache/spark/mllib/linalg/distributed/CoordinateMatrix.html)
 can be created from an `RDD[MatrixEntry]` instance, where
-[`MatrixEntry`](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.MatrixEntry) is a
+[`MatrixEntry`](api/scala/org/apache/spark/mllib/linalg/distributed/MatrixEntry.html) is a
 wrapper over `(Long, Long, Double)`.  A `CoordinateMatrix` can be converted to an `IndexedRowMatrix`
 with sparse rows by calling `toIndexedRowMatrix`.  Other computations for 
 `CoordinateMatrix` are not currently supported.
 
-Refer to the [`CoordinateMatrix` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.CoordinateMatrix) for details on the API.
+Refer to the [`CoordinateMatrix` Scala docs](api/scala/org/apache/spark/mllib/linalg/distributed/CoordinateMatrix.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.distributed.{CoordinateMatrix, MatrixEntry}
@@ -678,12 +678,12 @@ the sub-matrix at the given index with size `rowsPerBlock` x `colsPerBlock`.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-A [`BlockMatrix`](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.BlockMatrix) can be
+A [`BlockMatrix`](api/scala/org/apache/spark/mllib/linalg/distributed/BlockMatrix.html) can be
 most easily created from an `IndexedRowMatrix` or `CoordinateMatrix` by calling `toBlockMatrix`.
 `toBlockMatrix` creates blocks of size 1024 x 1024 by default.
 Users may change the block size by supplying the values through `toBlockMatrix(rowsPerBlock, colsPerBlock)`.
 
-Refer to the [`BlockMatrix` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.BlockMatrix) for details on the API.
+Refer to the [`BlockMatrix` Scala docs](api/scala/org/apache/spark/mllib/linalg/distributed/BlockMatrix.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.mllib.linalg.distributed.{BlockMatrix, CoordinateMatrix, MatrixEntry}
diff --git a/docs/mllib-decision-tree.md b/docs/mllib-decision-tree.md
index 045da74423..455649c8e6 100644
--- a/docs/mllib-decision-tree.md
+++ b/docs/mllib-decision-tree.md
@@ -151,7 +151,7 @@ When tuning these parameters, be careful to validate on held-out test data to av
 
 * **`maxDepth`**: Maximum depth of a tree.  Deeper trees are more expressive (potentially allowing higher accuracy), but they are also more costly to train and are more likely to overfit.
 
-* **`minInstancesPerNode`**: For a node to be split further, each of its children must receive at least this number of training instances.  This is commonly used with [RandomForest](api/scala/index.html#org.apache.spark.mllib.tree.RandomForest$) since those are often trained deeper than individual trees.
+* **`minInstancesPerNode`**: For a node to be split further, each of its children must receive at least this number of training instances.  This is commonly used with [RandomForest](api/scala/org/apache/spark/mllib/tree/RandomForest$.html) since those are often trained deeper than individual trees.
 
 * **`minInfoGain`**: For a node to be split further, the split must improve at least this much (in terms of information gain).
 
@@ -167,13 +167,13 @@ These parameters may be tuned.  Be careful to validate on held-out test data whe
   * The default value is conservatively chosen to be 256 MiB to allow the decision algorithm to work in most scenarios.  Increasing `maxMemoryInMB` can lead to faster training (if the memory is available) by allowing fewer passes over the data.  However, there may be decreasing returns as `maxMemoryInMB` grows since the amount of communication on each iteration can be proportional to `maxMemoryInMB`.
   * *Implementation details*: For faster processing, the decision tree algorithm collects statistics about groups of nodes to split (rather than 1 node at a time).  The number of nodes which can be handled in one group is determined by the memory requirements (which vary per features).  The `maxMemoryInMB` parameter specifies the memory limit in terms of megabytes which each worker can use for these statistics.
 
-* **`subsamplingRate`**: Fraction of the training data used for learning the decision tree.  This parameter is most relevant for training ensembles of trees (using [`RandomForest`](api/scala/index.html#org.apache.spark.mllib.tree.RandomForest$) and [`GradientBoostedTrees`](api/scala/index.html#org.apache.spark.mllib.tree.GradientBoostedTrees)), where it can be useful to subsample the original data.  For training a single decision tree, this parameter is less useful since the number of training instances is generally not the main constraint.
+* **`subsamplingRate`**: Fraction of the training data used for learning the decision tree.  This parameter is most relevant for training ensembles of trees (using [`RandomForest`](api/scala/org/apache/spark/mllib/tree/RandomForest$.html) and [`GradientBoostedTrees`](api/scala/org/apache/spark/mllib/tree/GradientBoostedTrees.html)), where it can be useful to subsample the original data.  For training a single decision tree, this parameter is less useful since the number of training instances is generally not the main constraint.
 
 * **`impurity`**: Impurity measure (discussed above) used to choose between candidate splits.  This measure must match the `algo` parameter.
 
 ### Caching and checkpointing
 
-MLlib 1.2 adds several features for scaling up to larger (deeper) trees and tree ensembles.  When `maxDepth` is set to be large, it can be useful to turn on node ID caching and checkpointing.  These parameters are also useful for [RandomForest](api/scala/index.html#org.apache.spark.mllib.tree.RandomForest$) when `numTrees` is set to be large.
+MLlib 1.2 adds several features for scaling up to larger (deeper) trees and tree ensembles.  When `maxDepth` is set to be large, it can be useful to turn on node ID caching and checkpointing.  These parameters are also useful for [RandomForest](api/scala/org/apache/spark/mllib/tree/RandomForest$.html) when `numTrees` is set to be large.
 
 * **`useNodeIdCache`**: If this is set to true, the algorithm will avoid passing the current model (tree or trees) to executors on each iteration.
   * This can be useful with deep trees (speeding up computation on workers) and for large Random Forests (reducing communication on each iteration).
@@ -207,7 +207,7 @@ maximum tree depth of 5. The test error is calculated to measure the algorithm a
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`DecisionTree` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree) and [`DecisionTreeModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.model.DecisionTreeModel) for details on the API.
+Refer to the [`DecisionTree` Scala docs](api/scala/org/apache/spark/mllib/tree/DecisionTree.html) and [`DecisionTreeModel` Scala docs](api/scala/org/apache/spark/mllib/tree/model/DecisionTreeModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/DecisionTreeClassificationExample.scala %}
 </div>
@@ -238,7 +238,7 @@ depth of 5. The Mean Squared Error (MSE) is computed at the end to evaluate
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`DecisionTree` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.DecisionTree) and [`DecisionTreeModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.model.DecisionTreeModel) for details on the API.
+Refer to the [`DecisionTree` Scala docs](api/scala/org/apache/spark/mllib/tree/DecisionTree.html) and [`DecisionTreeModel` Scala docs](api/scala/org/apache/spark/mllib/tree/model/DecisionTreeModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/DecisionTreeRegressionExample.scala %}
 </div>
diff --git a/docs/mllib-dimensionality-reduction.md b/docs/mllib-dimensionality-reduction.md
index 5eb36b4228..8818e403aa 100644
--- a/docs/mllib-dimensionality-reduction.md
+++ b/docs/mllib-dimensionality-reduction.md
@@ -77,7 +77,7 @@ passes, $O(n)$ storage on each executor, and $O(n k)$ storage on the driver.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`SingularValueDecomposition` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.SingularValueDecomposition) for details on the API.
+Refer to the [`SingularValueDecomposition` Scala docs](api/scala/org/apache/spark/mllib/linalg/SingularValueDecomposition.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/SVDExample.scala %}
 
@@ -117,14 +117,14 @@ the rotation matrix are called principal components. PCA is used widely in dimen
 The following code demonstrates how to compute principal components on a `RowMatrix`
 and use them to project the vectors into a low-dimensional space.
 
-Refer to the [`RowMatrix` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.distributed.RowMatrix) for details on the API.
+Refer to the [`RowMatrix` Scala docs](api/scala/org/apache/spark/mllib/linalg/distributed/RowMatrix.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/PCAOnRowMatrixExample.scala %}
 
 The following code demonstrates how to compute principal components on source vectors
 and use them to project the vectors into a low-dimensional space while keeping associated labels:
 
-Refer to the [`PCA` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.PCA) for details on the API.
+Refer to the [`PCA` Scala docs](api/scala/org/apache/spark/mllib/feature/PCA.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/PCAOnSourceVectorExample.scala %}
 
diff --git a/docs/mllib-ensembles.md b/docs/mllib-ensembles.md
index 6149f45821..27a9fe67f3 100644
--- a/docs/mllib-ensembles.md
+++ b/docs/mllib-ensembles.md
@@ -24,7 +24,7 @@ license: |
 
 An [ensemble method](http://en.wikipedia.org/wiki/Ensemble_learning)
 is a learning algorithm which creates a model composed of a set of other base models.
-`spark.mllib` supports two major ensemble algorithms: [`GradientBoostedTrees`](api/scala/index.html#org.apache.spark.mllib.tree.GradientBoostedTrees) and [`RandomForest`](api/scala/index.html#org.apache.spark.mllib.tree.RandomForest$).
+`spark.mllib` supports two major ensemble algorithms: [`GradientBoostedTrees`](api/scala/org/apache/spark/mllib/tree/GradientBoostedTrees.html) and [`RandomForest`](api/scala/org/apache/spark/mllib/tree/RandomForest$.html).
 Both use [decision trees](mllib-decision-tree.html) as their base models.
 
 ## Gradient-Boosted Trees vs. Random Forests
@@ -111,7 +111,7 @@ The test error is calculated to measure the algorithm accuracy.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`RandomForest` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.RandomForest$) and [`RandomForestModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.model.RandomForestModel) for details on the API.
+Refer to the [`RandomForest` Scala docs](api/scala/org/apache/spark/mllib/tree/RandomForest$.html) and [`RandomForestModel` Scala docs](api/scala/org/apache/spark/mllib/tree/model/RandomForestModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/RandomForestClassificationExample.scala %}
 </div>
@@ -142,7 +142,7 @@ The Mean Squared Error (MSE) is computed at the end to evaluate
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`RandomForest` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.RandomForest$) and [`RandomForestModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.model.RandomForestModel) for details on the API.
+Refer to the [`RandomForest` Scala docs](api/scala/org/apache/spark/mllib/tree/RandomForest$.html) and [`RandomForestModel` Scala docs](api/scala/org/apache/spark/mllib/tree/model/RandomForestModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/RandomForestRegressionExample.scala %}
 </div>
@@ -252,7 +252,7 @@ The test error is calculated to measure the algorithm accuracy.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`GradientBoostedTrees` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.GradientBoostedTrees) and [`GradientBoostedTreesModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.model.GradientBoostedTreesModel) for details on the API.
+Refer to the [`GradientBoostedTrees` Scala docs](api/scala/org/apache/spark/mllib/tree/GradientBoostedTrees.html) and [`GradientBoostedTreesModel` Scala docs](api/scala/org/apache/spark/mllib/tree/model/GradientBoostedTreesModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/GradientBoostingClassificationExample.scala %}
 </div>
@@ -283,7 +283,7 @@ The Mean Squared Error (MSE) is computed at the end to evaluate
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`GradientBoostedTrees` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.GradientBoostedTrees) and [`GradientBoostedTreesModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.tree.model.GradientBoostedTreesModel) for details on the API.
+Refer to the [`GradientBoostedTrees` Scala docs](api/scala/org/apache/spark/mllib/tree/GradientBoostedTrees.html) and [`GradientBoostedTreesModel` Scala docs](api/scala/org/apache/spark/mllib/tree/model/GradientBoostedTreesModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/GradientBoostingRegressionExample.scala %}
 </div>
diff --git a/docs/mllib-evaluation-metrics.md b/docs/mllib-evaluation-metrics.md
index fb2883de68..f9efa769fc 100644
--- a/docs/mllib-evaluation-metrics.md
+++ b/docs/mllib-evaluation-metrics.md
@@ -117,7 +117,7 @@ The following code snippets illustrate how to load a sample dataset, train a bin
 data, and evaluate the performance of the algorithm by several binary evaluation metrics.
 
 <div data-lang="scala" markdown="1">
-Refer to the [`LogisticRegressionWithLBFGS` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithLBFGS) and [`BinaryClassificationMetrics` Scala docs](api/scala/index.html#org.apache.spark.mllib.evaluation.BinaryClassificationMetrics) for details on the API.
+Refer to the [`LogisticRegressionWithLBFGS` Scala docs](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithLBFGS.html) and [`BinaryClassificationMetrics` Scala docs](api/scala/org/apache/spark/mllib/evaluation/BinaryClassificationMetrics.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/BinaryClassificationMetricsExample.scala %}
 
@@ -243,7 +243,7 @@ The following code snippets illustrate how to load a sample dataset, train a mul
 the data, and evaluate the performance of the algorithm by several multiclass classification evaluation metrics.
 
 <div data-lang="scala" markdown="1">
-Refer to the [`MulticlassMetrics` Scala docs](api/scala/index.html#org.apache.spark.mllib.evaluation.MulticlassMetrics) for details on the API.
+Refer to the [`MulticlassMetrics` Scala docs](api/scala/org/apache/spark/mllib/evaluation/MulticlassMetrics.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/MulticlassMetricsExample.scala %}
 
@@ -393,7 +393,7 @@ True classes:
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`MultilabelMetrics` Scala docs](api/scala/index.html#org.apache.spark.mllib.evaluation.MultilabelMetrics) for details on the API.
+Refer to the [`MultilabelMetrics` Scala docs](api/scala/org/apache/spark/mllib/evaluation/MultilabelMetrics.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/MultiLabelMetricsExample.scala %}
 
@@ -521,7 +521,7 @@ expanded world of non-positive weights are "the same as never having interacted
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`RegressionMetrics` Scala docs](api/scala/index.html#org.apache.spark.mllib.evaluation.RegressionMetrics) and [`RankingMetrics` Scala docs](api/scala/index.html#org.apache.spark.mllib.evaluation.RankingMetrics) for details on the API.
+Refer to the [`RegressionMetrics` Scala docs](api/scala/org/apache/spark/mllib/evaluation/RegressionMetrics.html) and [`RankingMetrics` Scala docs](api/scala/org/apache/spark/mllib/evaluation/RankingMetrics.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/RankingMetricsExample.scala %}
 
diff --git a/docs/mllib-feature-extraction.md b/docs/mllib-feature-extraction.md
index 33a223ad48..8df9699150 100644
--- a/docs/mllib-feature-extraction.md
+++ b/docs/mllib-feature-extraction.md
@@ -69,12 +69,12 @@ We refer users to the [Stanford NLP Group](http://nlp.stanford.edu/) and
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-TF and IDF are implemented in [HashingTF](api/scala/index.html#org.apache.spark.mllib.feature.HashingTF)
-and [IDF](api/scala/index.html#org.apache.spark.mllib.feature.IDF).
+TF and IDF are implemented in [HashingTF](api/scala/org/apache/spark/mllib/feature/HashingTF.html)
+and [IDF](api/scala/org/apache/spark/mllib/feature/IDF.html).
 `HashingTF` takes an `RDD[Iterable[_]]` as the input.
 Each record could be an iterable of strings or other types.
 
-Refer to the [`HashingTF` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.HashingTF) for details on the API.
+Refer to the [`HashingTF` Scala docs](api/scala/org/apache/spark/mllib/feature/HashingTF.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/TFIDFExample.scala %}
 </div>
@@ -135,7 +135,7 @@ Here we assume the extracted file is `text8` and in same directory as you run th
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`Word2Vec` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.Word2Vec) for details on the API.
+Refer to the [`Word2Vec` Scala docs](api/scala/org/apache/spark/mllib/feature/Word2Vec.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/Word2VecExample.scala %}
 </div>
@@ -159,19 +159,19 @@ against features with very large variances exerting an overly large influence du
 
 ### Model Fitting
 
-[`StandardScaler`](api/scala/index.html#org.apache.spark.mllib.feature.StandardScaler) has the
+[`StandardScaler`](api/scala/org/apache/spark/mllib/feature/StandardScaler.html) has the
 following parameters in the constructor:
 
 * `withMean` False by default. Centers the data with mean before scaling. It will build a dense
 output, so take care when applying to sparse input.
 * `withStd` True by default. Scales the data to unit standard deviation.
 
-We provide a [`fit`](api/scala/index.html#org.apache.spark.mllib.feature.StandardScaler) method in
+We provide a [`fit`](api/scala/org/apache/spark/mllib/feature/StandardScaler.html) method in
 `StandardScaler` which can take an input of `RDD[Vector]`, learn the summary statistics, and then
 return a model which can transform the input dataset into unit standard deviation and/or zero mean features
 depending how we configure the `StandardScaler`.
 
-This model implements [`VectorTransformer`](api/scala/index.html#org.apache.spark.mllib.feature.VectorTransformer)
+This model implements [`VectorTransformer`](api/scala/org/apache/spark/mllib/feature/VectorTransformer.html)
 which can apply the standardization on a `Vector` to produce a transformed `Vector` or on
 an `RDD[Vector]` to produce a transformed `RDD[Vector]`.
 
@@ -185,7 +185,7 @@ so that the new features have unit standard deviation and/or zero mean.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`StandardScaler` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.StandardScaler) for details on the API.
+Refer to the [`StandardScaler` Scala docs](api/scala/org/apache/spark/mllib/feature/StandardScaler.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/StandardScalerExample.scala %}
 </div>
@@ -203,12 +203,12 @@ Normalizer scales individual samples to have unit $L^p$ norm. This is a common o
 classification or clustering. For example, the dot product of two $L^2$ normalized TF-IDF vectors
 is the cosine similarity of the vectors.
 
-[`Normalizer`](api/scala/index.html#org.apache.spark.mllib.feature.Normalizer) has the following
+[`Normalizer`](api/scala/org/apache/spark/mllib/feature/Normalizer.html) has the following
 parameter in the constructor:
 
 * `p` Normalization in $L^p$ space, $p = 2$ by default.
 
-`Normalizer` implements [`VectorTransformer`](api/scala/index.html#org.apache.spark.mllib.feature.VectorTransformer)
+`Normalizer` implements [`VectorTransformer`](api/scala/org/apache/spark/mllib/feature/VectorTransformer.html)
 which can apply the normalization on a `Vector` to produce a transformed `Vector` or on
 an `RDD[Vector]` to produce a transformed `RDD[Vector]`.
 
@@ -221,7 +221,7 @@ with $L^2$ norm, and $L^\infty$ norm.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-Refer to the [`Normalizer` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.Normalizer) for details on the API.
+Refer to the [`Normalizer` Scala docs](api/scala/org/apache/spark/mllib/feature/Normalizer.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/NormalizerExample.scala %}
 </div>
@@ -239,7 +239,7 @@ Refer to the [`Normalizer` Python docs](api/python/pyspark.mllib.html#pyspark.ml
 features for use in model construction. It reduces the size of the feature space, which can improve
 both speed and statistical learning behavior.
 
-[`ChiSqSelector`](api/scala/index.html#org.apache.spark.mllib.feature.ChiSqSelector) implements
+[`ChiSqSelector`](api/scala/org/apache/spark/mllib/feature/ChiSqSelector.html) implements
 Chi-Squared feature selection. It operates on labeled data with categorical features. ChiSqSelector uses the
 [Chi-Squared test of independence](https://en.wikipedia.org/wiki/Chi-squared_test) to decide which
 features to choose. It supports five selection methods: `numTopFeatures`, `percentile`, `fpr`, `fdr`, `fwe`:
@@ -257,7 +257,7 @@ The number of features to select can be tuned using a held-out validation set.
 
 ### Model Fitting
 
-The [`fit`](api/scala/index.html#org.apache.spark.mllib.feature.ChiSqSelector) method takes
+The [`fit`](api/scala/org/apache/spark/mllib/feature/ChiSqSelector.html) method takes
 an input of `RDD[LabeledPoint]` with categorical features, learns the summary statistics, and then
 returns a `ChiSqSelectorModel` which can transform an input dataset into the reduced feature space.
 The `ChiSqSelectorModel` can be applied either to a `Vector` to produce a reduced `Vector`, or to
@@ -272,7 +272,7 @@ The following example shows the basic use of ChiSqSelector. The data set used ha
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [`ChiSqSelector` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.ChiSqSelector)
+Refer to the [`ChiSqSelector` Scala docs](api/scala/org/apache/spark/mllib/feature/ChiSqSelector.html)
 for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/ChiSqSelectorExample.scala %}
@@ -312,11 +312,11 @@ v_N
   \end{pmatrix}
 \]`
 
-[`ElementwiseProduct`](api/scala/index.html#org.apache.spark.mllib.feature.ElementwiseProduct) has the following parameter in the constructor:
+[`ElementwiseProduct`](api/scala/org/apache/spark/mllib/feature/ElementwiseProduct.html) has the following parameter in the constructor:
 
 * `scalingVec`: the transforming vector.
 
-`ElementwiseProduct` implements [`VectorTransformer`](api/scala/index.html#org.apache.spark.mllib.feature.VectorTransformer) which can apply the weighting on a `Vector` to produce a transformed `Vector` or on an `RDD[Vector]` to produce a transformed `RDD[Vector]`.
+`ElementwiseProduct` implements [`VectorTransformer`](api/scala/org/apache/spark/mllib/feature/VectorTransformer.html) which can apply the weighting on a `Vector` to produce a transformed `Vector` or on an `RDD[Vector]` to produce a transformed `RDD[Vector]`.
 
 ### Example
 
@@ -325,7 +325,7 @@ This example below demonstrates how to transform vectors using a transforming ve
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-Refer to the [`ElementwiseProduct` Scala docs](api/scala/index.html#org.apache.spark.mllib.feature.ElementwiseProduct) for details on the API.
+Refer to the [`ElementwiseProduct` Scala docs](api/scala/org/apache/spark/mllib/feature/ElementwiseProduct.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/ElementwiseProductExample.scala %}
 </div>
diff --git a/docs/mllib-frequent-pattern-mining.md b/docs/mllib-frequent-pattern-mining.md
index 8bc93ac2e8..709acde062 100644
--- a/docs/mllib-frequent-pattern-mining.md
+++ b/docs/mllib-frequent-pattern-mining.md
@@ -54,18 +54,18 @@ We refer users to the papers for more details.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-[`FPGrowth`](api/scala/index.html#org.apache.spark.mllib.fpm.FPGrowth) implements the
+[`FPGrowth`](api/scala/org/apache/spark/mllib/fpm/FPGrowth.html) implements the
 FP-growth algorithm.
 It takes an `RDD` of transactions, where each transaction is an `Array` of items of a generic type.
 Calling `FPGrowth.run` with transactions returns an
-[`FPGrowthModel`](api/scala/index.html#org.apache.spark.mllib.fpm.FPGrowthModel)
+[`FPGrowthModel`](api/scala/org/apache/spark/mllib/fpm/FPGrowthModel.html)
 that stores the frequent itemsets with their frequencies.  The following
 example illustrates how to mine frequent itemsets and association rules
 (see [Association
 Rules](mllib-frequent-pattern-mining.html#association-rules) for
 details) from `transactions`.
 
-Refer to the [`FPGrowth` Scala docs](api/scala/index.html#org.apache.spark.mllib.fpm.FPGrowth) for details on the API.
+Refer to the [`FPGrowth` Scala docs](api/scala/org/apache/spark/mllib/fpm/FPGrowth.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/SimpleFPGrowth.scala %}
 
@@ -111,7 +111,7 @@ Refer to the [`FPGrowth` Python docs](api/python/pyspark.mllib.html#pyspark.mlli
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[AssociationRules](api/scala/index.html#org.apache.spark.mllib.fpm.AssociationRules)
+[AssociationRules](api/scala/org/apache/spark/mllib/fpm/AssociationRules.html)
 implements a parallel rule generation algorithm for constructing rules
 that have a single item as the consequent.
 
@@ -168,13 +168,13 @@ The following example illustrates PrefixSpan running on the sequences
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-[`PrefixSpan`](api/scala/index.html#org.apache.spark.mllib.fpm.PrefixSpan) implements the
+[`PrefixSpan`](api/scala/org/apache/spark/mllib/fpm/PrefixSpan.html) implements the
 PrefixSpan algorithm.
 Calling `PrefixSpan.run` returns a
-[`PrefixSpanModel`](api/scala/index.html#org.apache.spark.mllib.fpm.PrefixSpanModel)
+[`PrefixSpanModel`](api/scala/org/apache/spark/mllib/fpm/PrefixSpanModel.html)
 that stores the frequent sequences with their frequencies.
 
-Refer to the [`PrefixSpan` Scala docs](api/scala/index.html#org.apache.spark.mllib.fpm.PrefixSpan) and [`PrefixSpanModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.fpm.PrefixSpanModel) for details on the API.
+Refer to the [`PrefixSpan` Scala docs](api/scala/org/apache/spark/mllib/fpm/PrefixSpan.html) and [`PrefixSpanModel` Scala docs](api/scala/org/apache/spark/mllib/fpm/PrefixSpanModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/PrefixSpanExample.scala %}
 
diff --git a/docs/mllib-isotonic-regression.md b/docs/mllib-isotonic-regression.md
index d9cc775547..94ffadaf65 100644
--- a/docs/mllib-isotonic-regression.md
+++ b/docs/mllib-isotonic-regression.md
@@ -74,7 +74,7 @@ i.e. 4710.28,500.00. The data are split to training and testing set.
 Model is created using the training set and a mean squared error is calculated from the predicted
 labels and real labels in the test set.
 
-Refer to the [`IsotonicRegression` Scala docs](api/scala/index.html#org.apache.spark.mllib.regression.IsotonicRegression) and [`IsotonicRegressionModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.regression.IsotonicRegressionModel) for details on the API.
+Refer to the [`IsotonicRegression` Scala docs](api/scala/org/apache/spark/mllib/regression/IsotonicRegression.html) and [`IsotonicRegressionModel` Scala docs](api/scala/org/apache/spark/mllib/regression/IsotonicRegressionModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/IsotonicRegressionExample.scala %}
 </div>
diff --git a/docs/mllib-linear-methods.md b/docs/mllib-linear-methods.md
index 801876dbff..e7726271cc 100644
--- a/docs/mllib-linear-methods.md
+++ b/docs/mllib-linear-methods.md
@@ -184,7 +184,7 @@ training algorithm on this training data using a static method in the algorithm
 object, and make predictions with the resulting model to compute the training
 error.
 
-Refer to the [`SVMWithSGD` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.SVMWithSGD) and [`SVMModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.SVMModel) for details on the API.
+Refer to the [`SVMWithSGD` Scala docs](api/scala/org/apache/spark/mllib/classification/SVMWithSGD.html) and [`SVMModel` Scala docs](api/scala/org/apache/spark/mllib/classification/SVMModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/SVMWithSGDExample.scala %}
 
@@ -305,11 +305,11 @@ We recommend L-BFGS over mini-batch gradient descent for faster convergence.
 <div data-lang="scala" markdown="1">
 The following code illustrates how to load a sample multiclass dataset, split it into train and
 test, and use
-[LogisticRegressionWithLBFGS](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithLBFGS)
+[LogisticRegressionWithLBFGS](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithLBFGS.html)
 to fit a logistic regression model.
 Then the model is evaluated against the test dataset and saved to disk.
 
-Refer to the [`LogisticRegressionWithLBFGS` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithLBFGS) and [`LogisticRegressionModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionModel) for details on the API.
+Refer to the [`LogisticRegressionWithLBFGS` Scala docs](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithLBFGS.html) and [`LogisticRegressionModel` Scala docs](api/scala/org/apache/spark/mllib/classification/LogisticRegressionModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/LogisticRegressionWithLBFGSExample.scala %}
 
@@ -438,8 +438,8 @@ regularization parameter (`regParam`) along with various parameters associated w
 gradient descent (`stepSize`, `numIterations`, `miniBatchFraction`).  For each of them, we support
 all three possible regularizations (none, L1 or L2).
 
-For Logistic Regression, [L-BFGS](api/scala/index.html#org.apache.spark.mllib.optimization.LBFGS)
-version is implemented under [LogisticRegressionWithLBFGS](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithLBFGS), and this
+For Logistic Regression, [L-BFGS](api/scala/org/apache/spark/mllib/optimization/LBFGS.html)
+version is implemented under [LogisticRegressionWithLBFGS](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithLBFGS.html), and this
 version supports both binary and multinomial Logistic Regression while SGD version only supports
 binary Logistic Regression. However, L-BFGS version doesn't support L1 regularization but SGD one
 supports L1 regularization. When L1 regularization is not required, L-BFGS version is strongly
@@ -448,10 +448,10 @@ inverse Hessian matrix using quasi-Newton method.
 
 Algorithms are all implemented in Scala:
 
-* [SVMWithSGD](api/scala/index.html#org.apache.spark.mllib.classification.SVMWithSGD)
-* [LogisticRegressionWithLBFGS](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithLBFGS)
-* [LogisticRegressionWithSGD](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithSGD)
-* [LinearRegressionWithSGD](api/scala/index.html#org.apache.spark.mllib.regression.LinearRegressionWithSGD)
-* [RidgeRegressionWithSGD](api/scala/index.html#org.apache.spark.mllib.regression.RidgeRegressionWithSGD)
-* [LassoWithSGD](api/scala/index.html#org.apache.spark.mllib.regression.LassoWithSGD)
+* [SVMWithSGD](api/scala/org/apache/spark/mllib/classification/SVMWithSGD.html)
+* [LogisticRegressionWithLBFGS](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithLBFGS.html)
+* [LogisticRegressionWithSGD](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithSGD.html)
+* [LinearRegressionWithSGD](api/scala/org/apache/spark/mllib/regression/LinearRegressionWithSGD.html)
+* [RidgeRegressionWithSGD](api/scala/org/apache/spark/mllib/regression/RidgeRegressionWithSGD.html)
+* [LassoWithSGD](api/scala/org/apache/spark/mllib/regression/LassoWithSGD.html)
 
diff --git a/docs/mllib-naive-bayes.md b/docs/mllib-naive-bayes.md
index 09b15876a3..a3602667b5 100644
--- a/docs/mllib-naive-bayes.md
+++ b/docs/mllib-naive-bayes.md
@@ -46,14 +46,14 @@ sparsity. Since the training data is only used once, it is not necessary to cach
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-[NaiveBayes](api/scala/index.html#org.apache.spark.mllib.classification.NaiveBayes$) implements
+[NaiveBayes](api/scala/org/apache/spark/mllib/classification/NaiveBayes$.html) implements
 multinomial naive Bayes. It takes an RDD of
-[LabeledPoint](api/scala/index.html#org.apache.spark.mllib.regression.LabeledPoint) and an optional
+[LabeledPoint](api/scala/org/apache/spark/mllib/regression/LabeledPoint.html) and an optional
 smoothing parameter `lambda` as input, an optional model type parameter (default is "multinomial"), and outputs a
-[NaiveBayesModel](api/scala/index.html#org.apache.spark.mllib.classification.NaiveBayesModel), which
+[NaiveBayesModel](api/scala/org/apache/spark/mllib/classification/NaiveBayesModel.html), which
 can be used for evaluation and prediction.
 
-Refer to the [`NaiveBayes` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.NaiveBayes) and [`NaiveBayesModel` Scala docs](api/scala/index.html#org.apache.spark.mllib.classification.NaiveBayesModel) for details on the API.
+Refer to the [`NaiveBayes` Scala docs](api/scala/org/apache/spark/mllib/classification/NaiveBayes$.html) and [`NaiveBayesModel` Scala docs](api/scala/org/apache/spark/mllib/classification/NaiveBayesModel.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/NaiveBayesExample.scala %}
 </div>
diff --git a/docs/mllib-optimization.md b/docs/mllib-optimization.md
index f2e128ec21..f0b0c817ed 100644
--- a/docs/mllib-optimization.md
+++ b/docs/mllib-optimization.md
@@ -111,12 +111,12 @@ As an alternative to just use the subgradient `$R'(\wv)$` of the regularizer in
 direction, an improved update for some cases can be obtained by using the proximal operator
 instead.
 For the L1-regularizer, the proximal operator is given by soft thresholding, as implemented in
-[L1Updater](api/scala/index.html#org.apache.spark.mllib.optimization.L1Updater).
+[L1Updater](api/scala/org/apache/spark/mllib/optimization/L1Updater.html).
 
 
 ### Update schemes for distributed SGD
 The SGD implementation in
-[GradientDescent](api/scala/index.html#org.apache.spark.mllib.optimization.GradientDescent) uses
+[GradientDescent](api/scala/org/apache/spark/mllib/optimization/GradientDescent.html) uses
 a simple (distributed) sampling of the data examples.
 We recall that the loss part of the optimization problem `$\eqref{eq:regPrimal}$` is
 `$\frac1n \sum_{i=1}^n L(\wv;\x_i,y_i)$`, and therefore `$\frac1n \sum_{i=1}^n L'_{\wv,i}$` would
@@ -169,7 +169,7 @@ are developed, see the
 section for example.
 
 The SGD class
-[GradientDescent](api/scala/index.html#org.apache.spark.mllib.optimization.GradientDescent)
+[GradientDescent](api/scala/org/apache/spark/mllib/optimization/GradientDescent.html)
 sets the following parameters:
 
 * `Gradient` is a class that computes the stochastic gradient of the function
@@ -195,15 +195,15 @@ each iteration, to compute the gradient direction.
 L-BFGS is currently only a low-level optimization primitive in `MLlib`. If you want to use L-BFGS in various 
 ML algorithms such as Linear Regression, and Logistic Regression, you have to pass the gradient of objective
 function, and updater into optimizer yourself instead of using the training APIs like 
-[LogisticRegressionWithSGD](api/scala/index.html#org.apache.spark.mllib.classification.LogisticRegressionWithSGD).
+[LogisticRegressionWithSGD](api/scala/org/apache/spark/mllib/classification/LogisticRegressionWithSGD.html).
 See the example below. It will be addressed in the next release. 
 
 The L1 regularization by using 
-[L1Updater](api/scala/index.html#org.apache.spark.mllib.optimization.L1Updater) will not work since the 
+[L1Updater](api/scala/org/apache/spark/mllib/optimization/L1Updater.html) will not work since the 
 soft-thresholding logic in L1Updater is designed for gradient descent. See the developer's note.
 
 The L-BFGS method
-[LBFGS.runLBFGS](api/scala/index.html#org.apache.spark.mllib.optimization.LBFGS)
+[LBFGS.runLBFGS](api/scala/org/apache/spark/mllib/optimization/LBFGS.html)
 has the following parameters:
 
 * `Gradient` is a class that computes the gradient of the objective function
@@ -233,7 +233,7 @@ L-BFGS optimizer.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-Refer to the [`LBFGS` Scala docs](api/scala/index.html#org.apache.spark.mllib.optimization.LBFGS) and [`SquaredL2Updater` Scala docs](api/scala/index.html#org.apache.spark.mllib.optimization.SquaredL2Updater) for details on the API.
+Refer to the [`LBFGS` Scala docs](api/scala/org/apache/spark/mllib/optimization/LBFGS.html) and [`SquaredL2Updater` Scala docs](api/scala/org/apache/spark/mllib/optimization/SquaredL2Updater.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/LBFGSExample.scala %}
 </div>
diff --git a/docs/mllib-pmml-model-export.md b/docs/mllib-pmml-model-export.md
index fbc14cefd1..d7eb51d69a 100644
--- a/docs/mllib-pmml-model-export.md
+++ b/docs/mllib-pmml-model-export.md
@@ -62,7 +62,7 @@ To export a supported `model` (see table above) to PMML, simply call `model.toPM
 
 As well as exporting the PMML model to a String (`model.toPMML` as in the example above), you can export the PMML model to other formats.
 
-Refer to the [`KMeans` Scala docs](api/scala/index.html#org.apache.spark.mllib.clustering.KMeans) and [`Vectors` Scala docs](api/scala/index.html#org.apache.spark.mllib.linalg.Vectors$) for details on the API.
+Refer to the [`KMeans` Scala docs](api/scala/org/apache/spark/mllib/clustering/KMeans.html) and [`Vectors` Scala docs](api/scala/org/apache/spark/mllib/linalg/Vectors$.html) for details on the API.
 
 Here a complete example of building a KMeansModel and print it out in PMML format:
 {% include_example scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala %}
diff --git a/docs/mllib-statistics.md b/docs/mllib-statistics.md
index 4698d3e634..7de214bb6b 100644
--- a/docs/mllib-statistics.md
+++ b/docs/mllib-statistics.md
@@ -48,12 +48,12 @@ available in `Statistics`.
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-[`colStats()`](api/scala/index.html#org.apache.spark.mllib.stat.Statistics$) returns an instance of
-[`MultivariateStatisticalSummary`](api/scala/index.html#org.apache.spark.mllib.stat.MultivariateStatisticalSummary),
+[`colStats()`](api/scala/org/apache/spark/mllib/stat/Statistics$.html) returns an instance of
+[`MultivariateStatisticalSummary`](api/scala/org/apache/spark/mllib/stat/MultivariateStatisticalSummary.html),
 which contains the column-wise max, min, mean, variance, and number of nonzeros, as well as the
 total count.
 
-Refer to the [`MultivariateStatisticalSummary` Scala docs](api/scala/index.html#org.apache.spark.mllib.stat.MultivariateStatisticalSummary) for details on the API.
+Refer to the [`MultivariateStatisticalSummary` Scala docs](api/scala/org/apache/spark/mllib/stat/MultivariateStatisticalSummary.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala %}
 </div>
@@ -91,11 +91,11 @@ correlation methods are currently Pearson's and Spearman's correlation.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`Statistics`](api/scala/index.html#org.apache.spark.mllib.stat.Statistics$) provides methods to
+[`Statistics`](api/scala/org/apache/spark/mllib/stat/Statistics$.html) provides methods to
 calculate correlations between series. Depending on the type of input, two `RDD[Double]`s or
 an `RDD[Vector]`, the output will be a `Double` or the correlation `Matrix` respectively.
 
-Refer to the [`Statistics` Scala docs](api/scala/index.html#org.apache.spark.mllib.stat.Statistics$) for details on the API.
+Refer to the [`Statistics` Scala docs](api/scala/org/apache/spark/mllib/stat/Statistics$.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/CorrelationsExample.scala %}
 </div>
@@ -137,7 +137,7 @@ python.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`sampleByKeyExact()`](api/scala/index.html#org.apache.spark.rdd.PairRDDFunctions) allows users to
+[`sampleByKeyExact()`](api/scala/org/apache/spark/rdd/PairRDDFunctions.html) allows users to
 sample exactly $\lceil f_k \cdot n_k \rceil \, \forall k \in K$ items, where $f_k$ is the desired
 fraction for key $k$, $n_k$ is the number of key-value pairs for key $k$, and $K$ is the set of
 keys. Sampling without replacement requires one additional pass over the RDD to guarantee sample
@@ -181,7 +181,7 @@ independence tests.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`Statistics`](api/scala/index.html#org.apache.spark.mllib.stat.Statistics$) provides methods to
+[`Statistics`](api/scala/org/apache/spark/mllib/stat/Statistics$.html) provides methods to
 run Pearson's chi-squared tests. The following example demonstrates how to run and interpret
 hypothesis tests.
 
@@ -221,11 +221,11 @@ message.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`Statistics`](api/scala/index.html#org.apache.spark.mllib.stat.Statistics$) provides methods to
+[`Statistics`](api/scala/org/apache/spark/mllib/stat/Statistics$.html) provides methods to
 run a 1-sample, 2-sided Kolmogorov-Smirnov test. The following example demonstrates how to run
 and interpret the hypothesis tests.
 
-Refer to the [`Statistics` Scala docs](api/scala/index.html#org.apache.spark.mllib.stat.Statistics$) for details on the API.
+Refer to the [`Statistics` Scala docs](api/scala/org/apache/spark/mllib/stat/Statistics$.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/HypothesisTestingKolmogorovSmirnovTestExample.scala %}
 </div>
@@ -269,7 +269,7 @@ all prior batches.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`StreamingTest`](api/scala/index.html#org.apache.spark.mllib.stat.test.StreamingTest)
+[`StreamingTest`](api/scala/org/apache/spark/mllib/stat/test/StreamingTest.html)
 provides streaming hypothesis testing.
 
 {% include_example scala/org/apache/spark/examples/mllib/StreamingTestExample.scala %}
@@ -292,12 +292,12 @@ uniform, standard normal, or Poisson.
 
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
-[`RandomRDDs`](api/scala/index.html#org.apache.spark.mllib.random.RandomRDDs$) provides factory
+[`RandomRDDs`](api/scala/org/apache/spark/mllib/random/RandomRDDs$.html) provides factory
 methods to generate random double RDDs or vector RDDs.
 The following example generates a random double RDD, whose values follows the standard normal
 distribution `N(0, 1)`, and then map it to `N(1, 4)`.
 
-Refer to the [`RandomRDDs` Scala docs](api/scala/index.html#org.apache.spark.mllib.random.RandomRDDs$) for details on the API.
+Refer to the [`RandomRDDs` Scala docs](api/scala/org/apache/spark/mllib/random/RandomRDDs$.html) for details on the API.
 
 {% highlight scala %}
 import org.apache.spark.SparkContext
@@ -370,11 +370,11 @@ mean of PDFs of normal distributions centered around each of the samples.
 <div class="codetabs">
 
 <div data-lang="scala" markdown="1">
-[`KernelDensity`](api/scala/index.html#org.apache.spark.mllib.stat.KernelDensity) provides methods
+[`KernelDensity`](api/scala/org/apache/spark/mllib/stat/KernelDensity.html) provides methods
 to compute kernel density estimates from an RDD of samples. The following example demonstrates how
 to do so.
 
-Refer to the [`KernelDensity` Scala docs](api/scala/index.html#org.apache.spark.mllib.stat.KernelDensity) for details on the API.
+Refer to the [`KernelDensity` Scala docs](api/scala/org/apache/spark/mllib/stat/KernelDensity.html) for details on the API.
 
 {% include_example scala/org/apache/spark/examples/mllib/KernelDensityEstimationExample.scala %}
 </div>
diff --git a/docs/quick-start.md b/docs/quick-start.md
index 93abb25f20..86ba2c44b0 100644
--- a/docs/quick-start.md
+++ b/docs/quick-start.md
@@ -57,7 +57,7 @@ scala> val textFile = spark.read.textFile("README.md")
 textFile: org.apache.spark.sql.Dataset[String] = [value: string]
 {% endhighlight %}
 
-You can get values from Dataset directly, by calling some actions, or transform the Dataset to get a new one. For more details, please read the _[API doc](api/scala/index.html#org.apache.spark.sql.Dataset)_.
+You can get values from Dataset directly, by calling some actions, or transform the Dataset to get a new one. For more details, please read the _[API doc](api/scala/org/apache/spark/sql/Dataset.html)_.
 
 {% highlight scala %}
 scala> textFile.count() // Number of items in this Dataset
diff --git a/docs/rdd-programming-guide.md b/docs/rdd-programming-guide.md
index 5e55c93c41..ba99007aaf 100644
--- a/docs/rdd-programming-guide.md
+++ b/docs/rdd-programming-guide.md
@@ -149,8 +149,8 @@ $ PYSPARK_PYTHON=/opt/pypy-2.5/bin/pypy bin/spark-submit examples/src/main/pytho
 
 <div data-lang="scala"  markdown="1">
 
-The first thing a Spark program must do is to create a [SparkContext](api/scala/index.html#org.apache.spark.SparkContext) object, which tells Spark
-how to access a cluster. To create a `SparkContext` you first need to build a [SparkConf](api/scala/index.html#org.apache.spark.SparkConf) object
+The first thing a Spark program must do is to create a [SparkContext](api/scala/org/apache/spark/SparkContext.html) object, which tells Spark
+how to access a cluster. To create a `SparkContext` you first need to build a [SparkConf](api/scala/org/apache/spark/SparkConf.html) object
 that contains information about your application.
 
 Only one SparkContext should be active per JVM. You must `stop()` the active SparkContext before creating a new one.
@@ -500,7 +500,7 @@ then this approach should work well for such cases.
 
 If you have custom serialized binary data (such as loading data from Cassandra / HBase), then you will first need to
 transform that data on the Scala/Java side to something which can be handled by Pyrolite's pickler.
-A [Converter](api/scala/index.html#org.apache.spark.api.python.Converter) trait is provided
+A [Converter](api/scala/org/apache/spark/api/python/Converter.html) trait is provided
 for this. Simply extend this trait and implement your transformation code in the ```convert```
 method. Remember to ensure that this class, along with any dependencies required to access your ```InputFormat```, are packaged into your Spark job jar and included on the PySpark
 classpath.
@@ -856,7 +856,7 @@ by a key.
 In Scala, these operations are automatically available on RDDs containing
 [Tuple2](http://www.scala-lang.org/api/{{site.SCALA_VERSION}}/index.html#scala.Tuple2) objects
 (the built-in tuples in the language, created by simply writing `(a, b)`). The key-value pair operations are available in the
-[PairRDDFunctions](api/scala/index.html#org.apache.spark.rdd.PairRDDFunctions) class,
+[PairRDDFunctions](api/scala/org/apache/spark/rdd/PairRDDFunctions.html) class,
 which automatically wraps around an RDD of tuples.
 
 For example, the following code uses the `reduceByKey` operation on key-value pairs to count how
@@ -946,12 +946,12 @@ We could also use `counts.sortByKey()`, for example, to sort the pairs alphabeti
 
 The following table lists some of the common transformations supported by Spark. Refer to the
 RDD API doc
-([Scala](api/scala/index.html#org.apache.spark.rdd.RDD),
+([Scala](api/scala/org/apache/spark/rdd/RDD.html),
  [Java](api/java/index.html?org/apache/spark/api/java/JavaRDD.html),
  [Python](api/python/pyspark.html#pyspark.RDD),
  [R](api/R/index.html))
 and pair RDD functions doc
-([Scala](api/scala/index.html#org.apache.spark.rdd.PairRDDFunctions),
+([Scala](api/scala/org/apache/spark/rdd/PairRDDFunctions.html),
  [Java](api/java/index.html?org/apache/spark/api/java/JavaPairRDD.html))
 for details.
 
@@ -1060,13 +1060,13 @@ for details.
 
 The following table lists some of the common actions supported by Spark. Refer to the
 RDD API doc
-([Scala](api/scala/index.html#org.apache.spark.rdd.RDD),
+([Scala](api/scala/org/apache/spark/rdd/RDD.html),
  [Java](api/java/index.html?org/apache/spark/api/java/JavaRDD.html),
  [Python](api/python/pyspark.html#pyspark.RDD),
  [R](api/R/index.html))
 
 and pair RDD functions doc
-([Scala](api/scala/index.html#org.apache.spark.rdd.PairRDDFunctions),
+([Scala](api/scala/org/apache/spark/rdd/PairRDDFunctions.html),
  [Java](api/java/index.html?org/apache/spark/api/java/JavaPairRDD.html))
 for details.
 
@@ -1208,7 +1208,7 @@ In addition, each persisted RDD can be stored using a different *storage level*,
 to persist the dataset on disk, persist it in memory but as serialized Java objects (to save space),
 replicate it across nodes.
 These levels are set by passing a
-`StorageLevel` object ([Scala](api/scala/index.html#org.apache.spark.storage.StorageLevel),
+`StorageLevel` object ([Scala](api/scala/org/apache/spark/storage/StorageLevel.html),
 [Java](api/java/index.html?org/apache/spark/storage/StorageLevel.html),
 [Python](api/python/pyspark.html#pyspark.StorageLevel))
 to `persist()`. The `cache()` method is a shorthand for using the default storage level,
@@ -1404,11 +1404,11 @@ res2: Long = 10
 {% endhighlight %}
 
 While this code used the built-in support for accumulators of type Long, programmers can also
-create their own types by subclassing [AccumulatorV2](api/scala/index.html#org.apache.spark.util.AccumulatorV2).
+create their own types by subclassing [AccumulatorV2](api/scala/org/apache/spark/util/AccumulatorV2.html).
 The AccumulatorV2 abstract class has several methods which one has to override: `reset` for resetting
 the accumulator to zero, `add` for adding another value into the accumulator,
 `merge` for merging another same-type accumulator into this one. Other methods that must be overridden
-are contained in the [API documentation](api/scala/index.html#org.apache.spark.util.AccumulatorV2). For example, supposing we had a `MyVector` class
+are contained in the [API documentation](api/scala/org/apache/spark/util/AccumulatorV2.html). For example, supposing we had a `MyVector` class
 representing mathematical vectors, we could write:
 
 {% highlight scala %}
@@ -1457,11 +1457,11 @@ accum.value();
 {% endhighlight %}
 
 While this code used the built-in support for accumulators of type Long, programmers can also
-create their own types by subclassing [AccumulatorV2](api/scala/index.html#org.apache.spark.util.AccumulatorV2).
+create their own types by subclassing [AccumulatorV2](api/scala/org/apache/spark/util/AccumulatorV2.html).
 The AccumulatorV2 abstract class has several methods which one has to override: `reset` for resetting
 the accumulator to zero, `add` for adding another value into the accumulator,
 `merge` for merging another same-type accumulator into this one. Other methods that must be overridden
-are contained in the [API documentation](api/scala/index.html#org.apache.spark.util.AccumulatorV2). For example, supposing we had a `MyVector` class
+are contained in the [API documentation](api/scala/org/apache/spark/util/AccumulatorV2.html). For example, supposing we had a `MyVector` class
 representing mathematical vectors, we could write:
 
 {% highlight java %}
@@ -1620,4 +1620,4 @@ For help on deploying, the [cluster mode overview](cluster-overview.html) descri
 in distributed operation and supported cluster managers.
 
 Finally, full API documentation is available in
-[Scala](api/scala/#org.apache.spark.package), [Java](api/java/), [Python](api/python/) and [R](api/R/).
+[Scala](api/scala/org/apache/spark/), [Java](api/java/), [Python](api/python/) and [R](api/R/).
diff --git a/docs/sql-data-sources-generic-options.md b/docs/sql-data-sources-generic-options.md
index 0cfe2ed1aa..6bcf48235b 100644
--- a/docs/sql-data-sources-generic-options.md
+++ b/docs/sql-data-sources-generic-options.md
@@ -118,4 +118,4 @@ To load all files recursively, you can use:
 <div data-lang="r"  markdown="1">
 {% include_example recursive_file_lookup r/RSparkSQLExample.R %}
 </div>
-</div>
\ No newline at end of file
+</div>
diff --git a/docs/sql-data-sources-jdbc.md b/docs/sql-data-sources-jdbc.md
index b0d37b11c7..3cdff42057 100644
--- a/docs/sql-data-sources-jdbc.md
+++ b/docs/sql-data-sources-jdbc.md
@@ -23,7 +23,7 @@ license: |
 {:toc}
 
 Spark SQL also includes a data source that can read data from other databases using JDBC. This
-functionality should be preferred over using [JdbcRDD](api/scala/index.html#org.apache.spark.rdd.JdbcRDD).
+functionality should be preferred over using [JdbcRDD](api/scala/org/apache/spark/rdd/JdbcRDD.html).
 This is because the results are returned
 as a DataFrame and they can easily be processed in Spark SQL or joined with other data sources.
 The JDBC data source is also easier to use from Java or Python as it does not require the user to
diff --git a/docs/sql-data-sources-json.md b/docs/sql-data-sources-json.md
index 4ce4897189..588f6cdaa0 100644
--- a/docs/sql-data-sources-json.md
+++ b/docs/sql-data-sources-json.md
@@ -93,4 +93,4 @@ SELECT * FROM jsonTable
 
 </div>
 
-</div>
\ No newline at end of file
+</div>
diff --git a/docs/sql-getting-started.md b/docs/sql-getting-started.md
index f637697a29..9df0f76826 100644
--- a/docs/sql-getting-started.md
+++ b/docs/sql-getting-started.md
@@ -27,7 +27,7 @@ license: |
 <div class="codetabs">
 <div data-lang="scala"  markdown="1">
 
-The entry point into all functionality in Spark is the [`SparkSession`](api/scala/index.html#org.apache.spark.sql.SparkSession) class. To create a basic `SparkSession`, just use `SparkSession.builder()`:
+The entry point into all functionality in Spark is the [`SparkSession`](api/scala/org/apache/spark/sql/SparkSession.html) class. To create a basic `SparkSession`, just use `SparkSession.builder()`:
 
 {% include_example init_session scala/org/apache/spark/examples/sql/SparkSQLExample.scala %}
 </div>
@@ -104,7 +104,7 @@ As an example, the following creates a DataFrame based on the content of a JSON
 
 ## Untyped Dataset Operations (aka DataFrame Operations)
 
-DataFrames provide a domain-specific language for structured data manipulation in [Scala](api/scala/index.html#org.apache.spark.sql.Dataset), [Java](api/java/index.html?org/apache/spark/sql/Dataset.html), [Python](api/python/pyspark.sql.html#pyspark.sql.DataFrame) and [R](api/R/SparkDataFrame.html).
+DataFrames provide a domain-specific language for structured data manipulation in [Scala](api/scala/org/apache/spark/sql/Dataset.html), [Java](api/java/index.html?org/apache/spark/sql/Dataset.html), [Python](api/python/pyspark.sql.html#pyspark.sql.DataFrame) and [R](api/R/SparkDataFrame.html).
 
 As mentioned above, in Spark 2.0, DataFrames are just Dataset of `Row`s in Scala and Java API. These operations are also referred as "untyped transformations" in contrast to "typed transformations" come with strongly typed Scala/Java Datasets.
 
@@ -114,9 +114,9 @@ Here we include some basic examples of structured data processing using Datasets
 <div data-lang="scala"  markdown="1">
 {% include_example untyped_ops scala/org/apache/spark/examples/sql/SparkSQLExample.scala %}
 
-For a complete list of the types of operations that can be performed on a Dataset, refer to the [API Documentation](api/scala/index.html#org.apache.spark.sql.Dataset).
+For a complete list of the types of operations that can be performed on a Dataset, refer to the [API Documentation](api/scala/org/apache/spark/sql/Dataset.html).
 
-In addition to simple column references and expressions, Datasets also have a rich library of functions including string manipulation, date arithmetic, common math operations and more. The complete list is available in the [DataFrame Function Reference](api/scala/index.html#org.apache.spark.sql.functions$).
+In addition to simple column references and expressions, Datasets also have a rich library of functions including string manipulation, date arithmetic, common math operations and more. The complete list is available in the [DataFrame Function Reference](api/scala/org/apache/spark/sql/functions$.html).
 </div>
 
 <div data-lang="java" markdown="1">
@@ -222,7 +222,7 @@ SELECT * FROM global_temp.temp_view
 ## Creating Datasets
 
 Datasets are similar to RDDs, however, instead of using Java serialization or Kryo they use
-a specialized [Encoder](api/scala/index.html#org.apache.spark.sql.Encoder) to serialize the objects
+a specialized [Encoder](api/scala/org/apache/spark/sql/Encoder.html) to serialize the objects
 for processing or transmitting over the network. While both encoders and standard serialization are
 responsible for turning an object into bytes, encoders are code generated dynamically and use a format
 that allows Spark to perform many operations like filtering, sorting and hashing without deserializing
@@ -351,16 +351,16 @@ For example:
 
 ## Aggregations
 
-The [built-in DataFrames functions](api/scala/index.html#org.apache.spark.sql.functions$) provide common
+The [built-in DataFrames functions](api/scala/org/apache/spark/sql/functions$.html) provide common
 aggregations such as `count()`, `countDistinct()`, `avg()`, `max()`, `min()`, etc.
 While those functions are designed for DataFrames, Spark SQL also has type-safe versions for some of them in
-[Scala](api/scala/index.html#org.apache.spark.sql.expressions.scalalang.typed$) and
+[Scala](api/scala/org/apache/spark/sql/expressions/scalalang/typed$.html) and
 [Java](api/java/org/apache/spark/sql/expressions/javalang/typed.html) to work with strongly typed Datasets.
 Moreover, users are not limited to the predefined aggregate functions and can create their own.
 
 ### Type-Safe User-Defined Aggregate Functions
 
-User-defined aggregations for strongly typed Datasets revolve around the [Aggregator](api/scala/index.html#org.apache.spark.sql.expressions.Aggregator) abstract class.
+User-defined aggregations for strongly typed Datasets revolve around the [Aggregator](api/scala/org/apache/spark/sql/expressions/Aggregator.html) abstract class.
 For example, a type-safe user-defined average can look like:
 
 <div class="codetabs">
diff --git a/docs/sql-migration-guide.md b/docs/sql-migration-guide.md
index 46b7416873..11afae14d0 100644
--- a/docs/sql-migration-guide.md
+++ b/docs/sql-migration-guide.md
@@ -737,11 +737,11 @@ and writing data out (`DataFrame.write`),
 and deprecated the old APIs (e.g., `SQLContext.parquetFile`, `SQLContext.jsonFile`).
 
 See the API docs for `SQLContext.read` (
-  <a href="api/scala/index.html#org.apache.spark.sql.SQLContext@read:DataFrameReader">Scala</a>,
+  <a href="api/scala/org/apache/spark/sql/SQLContext.html#read:DataFrameReader">Scala</a>,
   <a href="api/java/org/apache/spark/sql/SQLContext.html#read()">Java</a>,
   <a href="api/python/pyspark.sql.html#pyspark.sql.SQLContext.read">Python</a>
 ) and `DataFrame.write` (
-  <a href="api/scala/index.html#org.apache.spark.sql.DataFrame@write:DataFrameWriter">Scala</a>,
+  <a href="api/scala/org/apache/spark/sql/DataFrame.html#write:DataFrameWriter">Scala</a>,
   <a href="api/java/org/apache/spark/sql/Dataset.html#write()">Java</a>,
   <a href="api/python/pyspark.sql.html#pyspark.sql.DataFrame.write">Python</a>
 ) more information.
diff --git a/docs/sql-programming-guide.md b/docs/sql-programming-guide.md
index 0a4d07ea37..06bf553e4f 100644
--- a/docs/sql-programming-guide.md
+++ b/docs/sql-programming-guide.md
@@ -61,7 +61,7 @@ In Scala and Java, a DataFrame is represented by a Dataset of `Row`s.
 In [the Scala API][scala-datasets], `DataFrame` is simply a type alias of `Dataset[Row]`.
 While, in [Java API][java-datasets], users need to use `Dataset<Row>` to represent a `DataFrame`.
 
-[scala-datasets]: api/scala/index.html#org.apache.spark.sql.Dataset
+[scala-datasets]: api/scala/org/apache/spark/sql/Dataset.html
 [java-datasets]: api/java/index.html?org/apache/spark/sql/Dataset.html
 
 Throughout this document, we will often refer to Scala/Java Datasets of `Row`s as DataFrames.
diff --git a/docs/sql-ref-syntax-aux-analyze-table.md b/docs/sql-ref-syntax-aux-analyze-table.md
index e448ca38c8..40513e836b 100644
--- a/docs/sql-ref-syntax-aux-analyze-table.md
+++ b/docs/sql-ref-syntax-aux-analyze-table.md
@@ -106,4 +106,4 @@ ANALYZE TABLE table_identifier [ partition_spec ]
      max_col_len	13
      histogram	NULL
 
-{% endhighlight %}
\ No newline at end of file
+{% endhighlight %}
diff --git a/docs/sql-ref-syntax-aux-cache-refresh.md b/docs/sql-ref-syntax-aux-cache-refresh.md
index fea3100d96..4c56893aec 100644
--- a/docs/sql-ref-syntax-aux-cache-refresh.md
+++ b/docs/sql-ref-syntax-aux-cache-refresh.md
@@ -51,4 +51,4 @@ REFRESH "hdfs://path/to/table";
 - [CACHE TABLE](sql-ref-syntax-aux-cache-cache-table.html)
 - [CLEAR CACHE](sql-ref-syntax-aux-cache-clear-cache.html)
 - [UNCACHE TABLE](sql-ref-syntax-aux-cache-uncache-table.html)
-- [REFRESH TABLE](sql-ref-syntax-aux-refresh-table.html)
\ No newline at end of file
+- [REFRESH TABLE](sql-ref-syntax-aux-refresh-table.html)
diff --git a/docs/sql-ref-syntax-aux-refresh-table.md b/docs/sql-ref-syntax-aux-refresh-table.md
index 4b3fcdd65b..96d698a1d6 100644
--- a/docs/sql-ref-syntax-aux-refresh-table.md
+++ b/docs/sql-ref-syntax-aux-refresh-table.md
@@ -55,4 +55,4 @@ REFRESH TABLE tempDB.view1;
 ### Related Statements
 - [CACHE TABLE](sql-ref-syntax-aux-cache-cache-table.html)
 - [CLEAR CACHE](sql-ref-syntax-aux-cache-clear-cache.html)
-- [UNCACHE TABLE](sql-ref-syntax-aux-cache-uncache-table.html)
\ No newline at end of file
+- [UNCACHE TABLE](sql-ref-syntax-aux-cache-uncache-table.html)
diff --git a/docs/sql-ref-syntax-aux-resource-mgmt.md b/docs/sql-ref-syntax-aux-resource-mgmt.md
index 5eddb97938..0885f56bdb 100644
--- a/docs/sql-ref-syntax-aux-resource-mgmt.md
+++ b/docs/sql-ref-syntax-aux-resource-mgmt.md
@@ -22,4 +22,4 @@ license: |
 * [ADD FILE](sql-ref-syntax-aux-resource-mgmt-add-file.html)
 * [ADD JAR](sql-ref-syntax-aux-resource-mgmt-add-jar.html)
 * [LIST FILE](sql-ref-syntax-aux-resource-mgmt-list-file.html)
-* [LIST JAR](sql-ref-syntax-aux-resource-mgmt-list-jar.html)
\ No newline at end of file
+* [LIST JAR](sql-ref-syntax-aux-resource-mgmt-list-jar.html)
diff --git a/docs/sql-ref-syntax-aux-show-tables.md b/docs/sql-ref-syntax-aux-show-tables.md
index 41af8e7d60..2a078abf91 100644
--- a/docs/sql-ref-syntax-aux-show-tables.md
+++ b/docs/sql-ref-syntax-aux-show-tables.md
@@ -104,4 +104,4 @@ SHOW TABLES  LIKE 'sam*|suj';
 - [CREATE TABLE](sql-ref-syntax-ddl-create-table.html)
 - [DROP TABLE](sql-ref-syntax-ddl-drop-table.html)
 - [CREATE DATABASE](sql-ref-syntax-ddl-create-database.html)
-- [DROP DATABASE](sql-ref-syntax-ddl-drop-database.html)
\ No newline at end of file
+- [DROP DATABASE](sql-ref-syntax-ddl-drop-database.html)
diff --git a/docs/sql-ref-syntax-aux-show.md b/docs/sql-ref-syntax-aux-show.md
index ad5c3954c2..f6d700acf9 100644
--- a/docs/sql-ref-syntax-aux-show.md
+++ b/docs/sql-ref-syntax-aux-show.md
@@ -25,4 +25,4 @@ license: |
 * [SHOW TABLES](sql-ref-syntax-aux-show-tables.html)
 * [SHOW TBLPROPERTIES](sql-ref-syntax-aux-show-tblproperties.html)
 * [SHOW PARTITIONS](sql-ref-syntax-aux-show-partitions.html)
-* [SHOW CREATE TABLE](sql-ref-syntax-aux-show-create-table.html)
\ No newline at end of file
+* [SHOW CREATE TABLE](sql-ref-syntax-aux-show-create-table.html)
diff --git a/docs/sql-ref-syntax-ddl-drop-database.md b/docs/sql-ref-syntax-ddl-drop-database.md
index 68244648c9..0bdb98f2b1 100644
--- a/docs/sql-ref-syntax-ddl-drop-database.md
+++ b/docs/sql-ref-syntax-ddl-drop-database.md
@@ -77,4 +77,4 @@ DROP DATABASE IF EXISTS inventory_db CASCADE;
 ### Related statements
 - [CREATE DATABASE](sql-ref-syntax-ddl-create-database.html)
 - [DESCRIBE DATABASE](sql-ref-syntax-aux-describe-database.html)
-- [SHOW DATABASES](sql-ref-syntax-aux-show-databases.html)
\ No newline at end of file
+- [SHOW DATABASES](sql-ref-syntax-aux-show-databases.html)
diff --git a/docs/sql-ref-syntax-ddl-drop-function.md b/docs/sql-ref-syntax-ddl-drop-function.md
index a059960920..16d08d1ae8 100644
--- a/docs/sql-ref-syntax-ddl-drop-function.md
+++ b/docs/sql-ref-syntax-ddl-drop-function.md
@@ -102,4 +102,4 @@ DROP TEMPORARY FUNCTION IF EXISTS test_avg;
 ### Related statements
 - [CREATE FUNCTION](sql-ref-syntax-ddl-create-function.html)
 - [DESCRIBE FUNCTION](sql-ref-syntax-aux-describe-function.html)
-- [SHOW FUNCTION](sql-ref-syntax-aux-show-functions.html)
\ No newline at end of file
+- [SHOW FUNCTION](sql-ref-syntax-aux-show-functions.html)
diff --git a/docs/sql-ref-syntax-dml-insert-overwrite-directory-hive.md b/docs/sql-ref-syntax-dml-insert-overwrite-directory-hive.md
index 6d56cdeb05..3b0475aef1 100644
--- a/docs/sql-ref-syntax-dml-insert-overwrite-directory-hive.md
+++ b/docs/sql-ref-syntax-dml-insert-overwrite-directory-hive.md
@@ -84,4 +84,4 @@ INSERT OVERWRITE [ LOCAL ] DIRECTORY directory_path
 ### Related Statements
   * [INSERT INTO statement](sql-ref-syntax-dml-insert-into.html)
   * [INSERT OVERWRITE statement](sql-ref-syntax-dml-insert-overwrite-table.html)
-  * [INSERT OVERWRITE DIRECTORY statement](sql-ref-syntax-dml-insert-overwrite-directory.html)
\ No newline at end of file
+  * [INSERT OVERWRITE DIRECTORY statement](sql-ref-syntax-dml-insert-overwrite-directory.html)
diff --git a/docs/sql-ref-syntax-dml-insert-overwrite-directory.md b/docs/sql-ref-syntax-dml-insert-overwrite-directory.md
index 06000b593b..6f19c62bc3 100644
--- a/docs/sql-ref-syntax-dml-insert-overwrite-directory.md
+++ b/docs/sql-ref-syntax-dml-insert-overwrite-directory.md
@@ -82,4 +82,4 @@ INSERT OVERWRITE DIRECTORY
 ### Related Statements
   * [INSERT INTO statement](sql-ref-syntax-dml-insert-into.html)
   * [INSERT OVERWRITE statement](sql-ref-syntax-dml-insert-overwrite-table.html)
-  * [INSERT OVERWRITE DIRECTORY with Hive format statement](sql-ref-syntax-dml-insert-overwrite-directory-hive.html)
\ No newline at end of file
+  * [INSERT OVERWRITE DIRECTORY with Hive format statement](sql-ref-syntax-dml-insert-overwrite-directory-hive.html)
diff --git a/docs/sql-ref-syntax-dml.md b/docs/sql-ref-syntax-dml.md
index af09e20545..b5dd45f896 100644
--- a/docs/sql-ref-syntax-dml.md
+++ b/docs/sql-ref-syntax-dml.md
@@ -22,4 +22,4 @@ license: |
 Data Manipulation Statements are used to add, change, or delete data. Spark SQL supports the following Data Manipulation Statements:
 
 - [INSERT](sql-ref-syntax-dml-insert.html)
-- [LOAD](sql-ref-syntax-dml-load.html)
\ No newline at end of file
+- [LOAD](sql-ref-syntax-dml-load.html)
diff --git a/docs/sql-ref-syntax-qry-select-clusterby.md b/docs/sql-ref-syntax-qry-select-clusterby.md
index c96c441921..bb60e8bfe2 100644
--- a/docs/sql-ref-syntax-qry-select-clusterby.md
+++ b/docs/sql-ref-syntax-qry-select-clusterby.md
@@ -96,4 +96,4 @@ SELECT age, name FROM person CLUSTER BY age;
 - [ORDER BY Clause](sql-ref-syntax-qry-select-orderby.html)
 - [SORT BY Clause](sql-ref-syntax-qry-select-sortby.html)
 - [DISTRIBUTE BY Clause](sql-ref-syntax-qry-select-distribute-by.html)
-- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
\ No newline at end of file
+- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
diff --git a/docs/sql-ref-syntax-qry-select-distribute-by.md b/docs/sql-ref-syntax-qry-select-distribute-by.md
index e706ccf039..5ade9c16e4 100644
--- a/docs/sql-ref-syntax-qry-select-distribute-by.md
+++ b/docs/sql-ref-syntax-qry-select-distribute-by.md
@@ -91,4 +91,4 @@ SELECT age, name FROM person DISTRIBUTE BY age;
 - [ORDER BY Clause](sql-ref-syntax-qry-select-orderby.html)
 - [SORT BY Clause](sql-ref-syntax-qry-select-sortby.html)
 - [CLUSTER BY Clause](sql-ref-syntax-qry-select-clusterby.html)
-- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
\ No newline at end of file
+- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
diff --git a/docs/sql-ref-syntax-qry-select-sortby.md b/docs/sql-ref-syntax-qry-select-sortby.md
index c0a491b78e..1818a69f4a 100644
--- a/docs/sql-ref-syntax-qry-select-sortby.md
+++ b/docs/sql-ref-syntax-qry-select-sortby.md
@@ -184,4 +184,4 @@ SELECT /*+ REPARTITION(zip_code) */ name, age, zip_code FROM person
 - [ORDER BY Clause](sql-ref-syntax-qry-select-orderby.html)
 - [CLUSTER BY Clause](sql-ref-syntax-qry-select-clusterby.html)
 - [DISTRIBUTE BY Clause](sql-ref-syntax-qry-select-distribute-by.html)
-- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
\ No newline at end of file
+- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
diff --git a/docs/sql-ref-syntax-qry-select.md b/docs/sql-ref-syntax-qry-select.md
index 00bd719004..80b930f335 100644
--- a/docs/sql-ref-syntax-qry-select.md
+++ b/docs/sql-ref-syntax-qry-select.md
@@ -143,4 +143,4 @@ SELECT [ hints , ... ] [ ALL | DISTINCT ] { named_expression [ , ... ] }
 - [SORT BY Clause](sql-ref-syntax-qry-select-sortby.html)
 - [CLUSTER BY Clause](sql-ref-syntax-qry-select-clusterby.html)
 - [DISTRIBUTE BY Clause](sql-ref-syntax-qry-select-distribute-by.html)
-- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
\ No newline at end of file
+- [LIMIT Clause](sql-ref-syntax-qry-select-limit.html)
diff --git a/docs/streaming-custom-receivers.md b/docs/streaming-custom-receivers.md
index a37b961243..6ce73b27d1 100644
--- a/docs/streaming-custom-receivers.md
+++ b/docs/streaming-custom-receivers.md
@@ -28,7 +28,7 @@ in Scala or Java.
 ## Implementing a Custom Receiver
 
 This starts with implementing a **Receiver**
-([Scala doc](api/scala/index.html#org.apache.spark.streaming.receiver.Receiver),
+([Scala doc](api/scala/org/apache/spark/streaming/receiver/Receiver.html),
 [Java doc](api/java/org/apache/spark/streaming/receiver/Receiver.html)).
 A custom receiver must extend this abstract class by implementing two methods
 
diff --git a/docs/streaming-kafka-integration.md b/docs/streaming-kafka-integration.md
index 6fa363285f..3282124b0b 100644
--- a/docs/streaming-kafka-integration.md
+++ b/docs/streaming-kafka-integration.md
@@ -23,4 +23,4 @@ replicated commit log service.  Please read the [Kafka documentation](https://ka
 thoroughly before starting an integration using Spark.
 
 At the moment, Spark requires Kafka 0.10 and higher. See 
-<a href="streaming-kafka-0-10-integration.html">Kafka 0.10 integration documentation</a> for details.
\ No newline at end of file
+<a href="streaming-kafka-0-10-integration.html">Kafka 0.10 integration documentation</a> for details.
diff --git a/docs/streaming-kinesis-integration.md b/docs/streaming-kinesis-integration.md
index 3389d453c2..c81597160c 100644
--- a/docs/streaming-kinesis-integration.md
+++ b/docs/streaming-kinesis-integration.md
@@ -59,7 +59,7 @@ A Kinesis stream can be set up at one of the valid Kinesis endpoints with 1 or m
                 .storageLevel(StorageLevel.MEMORY_AND_DISK_2)
                 .build()
 
-	See the [API docs](api/scala/index.html#org.apache.spark.streaming.kinesis.KinesisInputDStream)
+	See the [API docs](api/scala/org/apache/spark/streaming/kinesis/KinesisInputDStream.html)
 	and the [example]({{site.SPARK_GITHUB_URL}}/tree/master/external/kinesis-asl/src/main/scala/org/apache/spark/examples/streaming/KinesisWordCountASL.scala). Refer to the [Running the Example](#running-the-example) subsection for instructions on how to run the example.
 
 	</div>
diff --git a/docs/streaming-programming-guide.md b/docs/streaming-programming-guide.md
index f6b579fbf7..ac4aa9255a 100644
--- a/docs/streaming-programming-guide.md
+++ b/docs/streaming-programming-guide.md
@@ -57,7 +57,7 @@ Spark Streaming provides a high-level abstraction called *discretized stream* or
 which represents a continuous stream of data. DStreams can be created either from input data
 streams from sources such as Kafka, and Kinesis, or by applying high-level
 operations on other DStreams. Internally, a DStream is represented as a sequence of
-[RDDs](api/scala/index.html#org.apache.spark.rdd.RDD).
+[RDDs](api/scala/org/apache/spark/rdd/RDD.html).
 
 This guide shows you how to start writing Spark Streaming programs with DStreams. You can
 write Spark Streaming programs in Scala, Java or Python (introduced in Spark 1.2),
@@ -80,7 +80,7 @@ do is as follows.
 <div data-lang="scala"  markdown="1" >
 First, we import the names of the Spark Streaming classes and some implicit
 conversions from StreamingContext into our environment in order to add useful methods to
-other classes we need (like DStream). [StreamingContext](api/scala/index.html#org.apache.spark.streaming.StreamingContext) is the
+other classes we need (like DStream). [StreamingContext](api/scala/org/apache/spark/streaming/StreamingContext.html) is the
 main entry point for all streaming functionality. We create a local StreamingContext with two execution threads,  and a batch interval of 1 second.
 
 {% highlight scala %}
@@ -185,7 +185,7 @@ JavaDStream<String> words = lines.flatMap(x -> Arrays.asList(x.split(" ")).itera
 generating multiple new records from each record in the source DStream. In this case,
 each line will be split into multiple words and the stream of words is represented as the
 `words` DStream. Note that we defined the transformation using a
-[FlatMapFunction](api/scala/index.html#org.apache.spark.api.java.function.FlatMapFunction) object.
+[FlatMapFunction](api/scala/org/apache/spark/api/java/function/FlatMapFunction.html) object.
 As we will discover along the way, there are a number of such convenience classes in the Java API
 that help defines DStream transformations.
 
@@ -201,9 +201,9 @@ wordCounts.print();
 {% endhighlight %}
 
 The `words` DStream is further mapped (one-to-one transformation) to a DStream of `(word,
-1)` pairs, using a [PairFunction](api/scala/index.html#org.apache.spark.api.java.function.PairFunction)
+1)` pairs, using a [PairFunction](api/scala/org/apache/spark/api/java/function/PairFunction.html)
 object. Then, it is reduced to get the frequency of words in each batch of data,
-using a [Function2](api/scala/index.html#org.apache.spark.api.java.function.Function2) object.
+using a [Function2](api/scala/org/apache/spark/api/java/function/Function2.html) object.
 Finally, `wordCounts.print()` will print a few of the counts generated every second.
 
 Note that when these lines are executed, Spark Streaming only sets up the computation it
@@ -435,7 +435,7 @@ To initialize a Spark Streaming program, a **StreamingContext** object has to be
 <div class="codetabs">
 <div data-lang="scala" markdown="1">
 
-A [StreamingContext](api/scala/index.html#org.apache.spark.streaming.StreamingContext) object can be created from a [SparkConf](api/scala/index.html#org.apache.spark.SparkConf) object.
+A [StreamingContext](api/scala/org/apache/spark/streaming/StreamingContext.html) object can be created from a [SparkConf](api/scala/org/apache/spark/SparkConf.html) object.
 
 {% highlight scala %}
 import org.apache.spark._
@@ -451,7 +451,7 @@ or a special __"local[\*]"__ string to run in local mode. In practice, when runn
 you will not want to hardcode `master` in the program,
 but rather [launch the application with `spark-submit`](submitting-applications.html) and
 receive it there. However, for local testing and unit tests, you can pass "local[\*]" to run Spark Streaming
-in-process (detects the number of cores in the local system). Note that this internally creates a [SparkContext](api/scala/index.html#org.apache.spark.SparkContext) (starting point of all Spark functionality) which can be accessed as `ssc.sparkContext`.
+in-process (detects the number of cores in the local system). Note that this internally creates a [SparkContext](api/scala/org/apache/spark/SparkContext.html) (starting point of all Spark functionality) which can be accessed as `ssc.sparkContext`.
 
 The batch interval must be set based on the latency requirements of your application
 and available cluster resources. See the [Performance Tuning](#setting-the-right-batch-interval)
@@ -584,7 +584,7 @@ Input DStreams are DStreams representing the stream of input data received from
 sources. In the [quick example](#a-quick-example), `lines` was an input DStream as it represented
 the stream of data received from the netcat server. Every input DStream
 (except file stream, discussed later in this section) is associated with a **Receiver**
-([Scala doc](api/scala/index.html#org.apache.spark.streaming.receiver.Receiver),
+([Scala doc](api/scala/org/apache/spark/streaming/receiver/Receiver.html),
 [Java doc](api/java/org/apache/spark/streaming/receiver/Receiver.html)) object which receives the
 data from a source and stores it in Spark's memory for processing.
 
@@ -739,7 +739,7 @@ DStreams can be created with data streams received through custom receivers. See
 For testing a Spark Streaming application with test data, one can also create a DStream based on a queue of RDDs, using `streamingContext.queueStream(queueOfRDDs)`. Each RDD pushed into the queue will be treated as a batch of data in the DStream, and processed like a stream.
 
 For more details on streams from sockets and files, see the API documentations of the relevant functions in
-[StreamingContext](api/scala/index.html#org.apache.spark.streaming.StreamingContext) for
+[StreamingContext](api/scala/org/apache/spark/streaming/StreamingContext.html) for
 Scala, [JavaStreamingContext](api/java/index.html?org/apache/spark/streaming/api/java/JavaStreamingContext.html)
 for Java, and [StreamingContext](api/python/pyspark.streaming.html#pyspark.streaming.StreamingContext) for Python.
 
@@ -1219,8 +1219,8 @@ joinedStream = windowedStream.transform(lambda rdd: rdd.join(dataset))
 In fact, you can also dynamically change the dataset you want to join against. The function provided to `transform` is evaluated every batch interval and therefore will use the current dataset that `dataset` reference points to.
 
 The complete list of DStream transformations is available in the API documentation. For the Scala API,
-see [DStream](api/scala/index.html#org.apache.spark.streaming.dstream.DStream)
-and [PairDStreamFunctions](api/scala/index.html#org.apache.spark.streaming.dstream.PairDStreamFunctions).
+see [DStream](api/scala/org/apache/spark/streaming/dstream/DStream.html)
+and [PairDStreamFunctions](api/scala/org/apache/spark/streaming/dstream/PairDStreamFunctions.html).
 For the Java API, see [JavaDStream](api/java/index.html?org/apache/spark/streaming/api/java/JavaDStream.html)
 and [JavaPairDStream](api/java/index.html?org/apache/spark/streaming/api/java/JavaPairDStream.html).
 For the Python API, see [DStream](api/python/pyspark.streaming.html#pyspark.streaming.DStream).
@@ -2067,7 +2067,7 @@ for prime time, the old one be can be brought down. Note that this can be done f
 sending the data to two destinations (i.e., the earlier and upgraded applications).
 
 - The existing application is shutdown gracefully (see
-[`StreamingContext.stop(...)`](api/scala/index.html#org.apache.spark.streaming.StreamingContext)
+[`StreamingContext.stop(...)`](api/scala/org/apache/spark/streaming/StreamingContext.html)
 or [`JavaStreamingContext.stop(...)`](api/java/index.html?org/apache/spark/streaming/api/java/JavaStreamingContext.html)
 for graceful shutdown options) which ensure data that has been received is completely
 processed before shutdown. Then the
@@ -2104,7 +2104,7 @@ In that case, consider
 [reducing](#reducing-the-batch-processing-times) the batch processing time.
 
 The progress of a Spark Streaming program can also be monitored using the
-[StreamingListener](api/scala/index.html#org.apache.spark.streaming.scheduler.StreamingListener) interface,
+[StreamingListener](api/scala/org/apache/spark/streaming/scheduler/StreamingListener.html) interface,
 which allows you to get receiver status and processing times. Note that this is a developer API
 and it is likely to be improved upon (i.e., more information reported) in the future.
 
@@ -2197,7 +2197,7 @@ computation is not high enough. For example, for distributed reduce operations l
 and `reduceByKeyAndWindow`, the default number of parallel tasks is controlled by
 the `spark.default.parallelism` [configuration property](configuration.html#spark-properties). You
 can pass the level of parallelism as an argument (see
-[`PairDStreamFunctions`](api/scala/index.html#org.apache.spark.streaming.dstream.PairDStreamFunctions)
+[`PairDStreamFunctions`](api/scala/org/apache/spark/streaming/dstream/PairDStreamFunctions.html)
 documentation), or set the `spark.default.parallelism`
 [configuration property](configuration.html#spark-properties) to change the default.
 
@@ -2205,9 +2205,9 @@ documentation), or set the `spark.default.parallelism`
 {:.no_toc}
 The overheads of data serialization can be reduced by tuning the serialization formats. In the case of streaming, there are two types of data that are being serialized.
 
-* **Input data**: By default, the input data received through Receivers is stored in the executors' memory with [StorageLevel.MEMORY_AND_DISK_SER_2](api/scala/index.html#org.apache.spark.storage.StorageLevel$). That is, the data is serialized into bytes to reduce GC overheads, and replicated for tolerating executor failures. Also, the data is kept first in memory, and spilled over to disk only if the memory is insufficient to hold all of the input data necessary for the streaming computation. This serialization obviously has overheads -- the receiver must deserialize the received data and re-serialize it using Spark's serialization format. 
+* **Input data**: By default, the input data received through Receivers is stored in the executors' memory with [StorageLevel.MEMORY_AND_DISK_SER_2](api/scala/org/apache/spark/storage/StorageLevel$.html). That is, the data is serialized into bytes to reduce GC overheads, and replicated for tolerating executor failures. Also, the data is kept first in memory, and spilled over to disk only if the memory is insufficient to hold all of the input data necessary for the streaming computation. This serialization obviously has overheads -- the receiver must deserialize the received data and re-serialize it using Spark's serialization format.
 
-* **Persisted RDDs generated by Streaming Operations**: RDDs generated by streaming computations may be persisted in memory. For example, window operations persist data in memory as they would be processed multiple times. However, unlike the Spark Core default of [StorageLevel.MEMORY_ONLY](api/scala/index.html#org.apache.spark.storage.StorageLevel$), persisted RDDs generated by streaming computations are persisted with [StorageLevel.MEMORY_ONLY_SER](api/scala/index.html#org.apache.spark.storage.StorageLevel$) (i.e. serialized) by default to minimize GC overheads.
+* **Persisted RDDs generated by Streaming Operations**: RDDs generated by streaming computations may be persisted in memory. For example, window operations persist data in memory as they would be processed multiple times. However, unlike the Spark Core default of [StorageLevel.MEMORY_ONLY](api/scala/org/apache/spark/storage/StorageLevel$.html), persisted RDDs generated by streaming computations are persisted with [StorageLevel.MEMORY_ONLY_SER](api/scala/org/apache/spark/storage/StorageLevel.html$) (i.e. serialized) by default to minimize GC overheads.
 
 In both cases, using Kryo serialization can reduce both CPU and memory overheads. See the [Spark Tuning Guide](tuning.html#data-serialization) for more details. For Kryo, consider registering custom classes, and disabling object reference tracking (see Kryo-related configurations in the [Configuration Guide](configuration.html#compression-and-serialization)).
 
@@ -2247,7 +2247,7 @@ A good approach to figure out the right batch size for your application is to te
 conservative batch interval (say, 5-10 seconds) and a low data rate. To verify whether the system
 is able to keep up with the data rate, you can check the value of the end-to-end delay experienced
 by each processed batch (either look for "Total delay" in Spark driver log4j logs, or use the
-[StreamingListener](api/scala/index.html#org.apache.spark.streaming.scheduler.StreamingListener)
+[StreamingListener](api/scala/org/apache/spark/streaming/scheduler/StreamingListener.html)
 interface).
 If the delay is maintained to be comparable to the batch size, then system is stable. Otherwise,
 if the delay is continuously increasing, it means that the system is unable to keep up and it
@@ -2485,10 +2485,10 @@ additional effort may be necessary to achieve exactly-once semantics. There are
 * Third-party DStream data sources can be found in [Third Party Projects](https://spark.apache.org/third-party-projects.html)
 * API documentation
   - Scala docs
-    * [StreamingContext](api/scala/index.html#org.apache.spark.streaming.StreamingContext) and
-  [DStream](api/scala/index.html#org.apache.spark.streaming.dstream.DStream)
-    * [KafkaUtils](api/scala/index.html#org.apache.spark.streaming.kafka.KafkaUtils$),
-    [KinesisUtils](api/scala/index.html#org.apache.spark.streaming.kinesis.KinesisInputDStream),
+    * [StreamingContext](api/scala/org/apache/spark/streaming/StreamingContext.html) and
+  [DStream](api/scala/org/apache/spark/streaming/dstream/DStream.html)
+    * [KafkaUtils](api/scala/org/apache/spark/streaming/kafka/KafkaUtils$.html),
+    [KinesisUtils](api/scala/org/apache/spark/streaming/kinesis/KinesisInputDStream.html),
   - Java docs
     * [JavaStreamingContext](api/java/index.html?org/apache/spark/streaming/api/java/JavaStreamingContext.html),
     [JavaDStream](api/java/index.html?org/apache/spark/streaming/api/java/JavaDStream.html) and
diff --git a/docs/structured-streaming-programming-guide.md b/docs/structured-streaming-programming-guide.md
index 727bda18a1..9f4edd73c2 100644
--- a/docs/structured-streaming-programming-guide.md
+++ b/docs/structured-streaming-programming-guide.md
@@ -498,13 +498,13 @@ to track the read position in the stream. The engine uses checkpointing and writ
 
 # API using Datasets and DataFrames
 Since Spark 2.0, DataFrames and Datasets can represent static, bounded data, as well as streaming, unbounded data. Similar to static Datasets/DataFrames, you can use the common entry point `SparkSession`
-([Scala](api/scala/index.html#org.apache.spark.sql.SparkSession)/[Java](api/java/org/apache/spark/sql/SparkSession.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.SparkSession)/[R](api/R/sparkR.session.html) docs)
+([Scala](api/scala/org/apache/spark/sql/SparkSession.html)/[Java](api/java/org/apache/spark/sql/SparkSession.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.SparkSession)/[R](api/R/sparkR.session.html) docs)
 to create streaming DataFrames/Datasets from streaming sources, and apply the same operations on them as static DataFrames/Datasets. If you are not familiar with Datasets/DataFrames, you are strongly advised to familiarize yourself with them using the
 [DataFrame/Dataset Programming Guide](sql-programming-guide.html).
 
 ## Creating streaming DataFrames and streaming Datasets
 Streaming DataFrames can be created through the `DataStreamReader` interface
-([Scala](api/scala/index.html#org.apache.spark.sql.streaming.DataStreamReader)/[Java](api/java/org/apache/spark/sql/streaming/DataStreamReader.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.streaming.DataStreamReader) docs)
+([Scala](api/scala/org/apache/spark/sql/streaming/DataStreamReader.html)/[Java](api/java/org/apache/spark/sql/streaming/DataStreamReader.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.streaming.DataStreamReader) docs)
 returned by `SparkSession.readStream()`. In [R](api/R/read.stream.html), with the `read.stream()` method. Similar to the read interface for creating static DataFrame, you can specify the details of the source – data format, schema, options, etc.
 
 #### Input Sources
@@ -557,7 +557,7 @@ Here are the details of all the sources in Spark.
         NOTE 3: Both delete and move actions are best effort. Failing to delete or move files will not fail the streaming query. Spark may not clean up some source files in some circumstances - e.g. the application doesn't shut down gracefully, too many files are queued to clean up.
         <br/><br/>
         For file-format-specific options, see the related methods in <code>DataStreamReader</code>
-        (<a href="api/scala/index.html#org.apache.spark.sql.streaming.DataStreamReader">Scala</a>/<a href="api/java/org/apache/spark/sql/streaming/DataStreamReader.html">Java</a>/<a href="api/python/pyspark.sql.html#pyspark.sql.streaming.DataStreamReader">Python</a>/<a
+        (<a href="api/scala/org/apache/spark/sql/streaming/DataStreamReader.html">Scala</a>/<a href="api/java/org/apache/spark/sql/streaming/DataStreamReader.html">Java</a>/<a href="api/python/pyspark.sql.html#pyspark.sql.streaming.DataStreamReader">Python</a>/<a
         href="api/R/read.stream.html">R</a>).
         E.g. for "parquet" format options see <code>DataStreamReader.parquet()</code>.
         <br/><br/>
@@ -1622,7 +1622,7 @@ However, as a side effect, data from the slower streams will be aggressively dro
 this configuration judiciously.
 
 ### Arbitrary Stateful Operations
-Many usecases require more advanced stateful operations than aggregations. For example, in many usecases, you have to track sessions from data streams of events. For doing such sessionization, you will have to save arbitrary types of data as state, and perform arbitrary operations on the state using the data stream events in every trigger. Since Spark 2.2, this can be done using the operation `mapGroupsWithState` and the more powerful operation `flatMapGroupsWithState`. Both operations allow you to apply user-defined code on grouped Datasets to update user-defined state. For more concrete details, take a look at the API documentation ([Scala](api/scala/index.html#org.apache.spark.sql.streaming.GroupState)/[Java](api/java/org/apache/spark/sql/streaming/GroupState.html)) and the examples ([Scala]({{site.SPARK_GITHUB_URL}}/blob/v{{site.SPARK_VERSION_SHORT}}/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala)/[Java]({{site.SPARK_GITHUB_URL}}/blob/v{{site.SPARK_VERSION_SHORT}}/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredSessionization.java)).
+Many usecases require more advanced stateful operations than aggregations. For example, in many usecases, you have to track sessions from data streams of events. For doing such sessionization, you will have to save arbitrary types of data as state, and perform arbitrary operations on the state using the data stream events in every trigger. Since Spark 2.2, this can be done using the operation `mapGroupsWithState` and the more powerful operation `flatMapGroupsWithState`. Both operations allow you to apply user-defined code on grouped Datasets to update user-defined state. For more concrete details, take a look at the API documentation ([Scala](api/scala/org/apache/spark/sql/streaming/GroupState.html)/[Java](api/java/org/apache/spark/sql/streaming/GroupState.html)) and the examples ([Scala]({{site.SPARK_GITHUB_URL}}/blob/v{{site.SPARK_VERSION_SHORT}}/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala)/[Java]({{site.SPARK_GITHUB_URL}}/blob/v{{site.SPARK_VERSION_SHORT}}/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredSessionization.java)).
 
 Though Spark cannot check and force it, the state function should be implemented with respect to the semantics of the output mode. For example, in Update mode Spark doesn't expect that the state function will emit rows which are older than current watermark plus allowed late record delay, whereas in Append mode the state function can emit these rows.
 
@@ -1679,7 +1679,7 @@ end-to-end exactly once per query. Ensuring end-to-end exactly once for the last
 
 ## Starting Streaming Queries
 Once you have defined the final result DataFrame/Dataset, all that is left is for you to start the streaming computation. To do that, you have to use the `DataStreamWriter`
-([Scala](api/scala/index.html#org.apache.spark.sql.streaming.DataStreamWriter)/[Java](api/java/org/apache/spark/sql/streaming/DataStreamWriter.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.streaming.DataStreamWriter) docs)
+([Scala](api/scala/org/apache/spark/sql/streaming/DataStreamWriter.html)/[Java](api/java/org/apache/spark/sql/streaming/DataStreamWriter.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.streaming.DataStreamWriter) docs)
 returned through `Dataset.writeStream()`. You will have to specify one or more of the following in this interface.
 
 - *Details of the output sink:* Data format, location, etc.
@@ -1863,7 +1863,7 @@ Here are the details of all the sinks in Spark.
         <code>path</code>: path to the output directory, must be specified.
         <br/><br/>
         For file-format-specific options, see the related methods in DataFrameWriter
-        (<a href="api/scala/index.html#org.apache.spark.sql.DataFrameWriter">Scala</a>/<a href="api/java/org/apache/spark/sql/DataFrameWriter.html">Java</a>/<a href="api/python/pyspark.sql.html#pyspark.sql.DataFrameWriter">Python</a>/<a
+        (<a href="api/scala/org/apache/spark/sql/DataFrameWriter.html">Scala</a>/<a href="api/java/org/apache/spark/sql/DataFrameWriter.html">Java</a>/<a href="api/python/pyspark.sql.html#pyspark.sql.DataFrameWriter">Python</a>/<a
         href="api/R/write.stream.html">R</a>).
         E.g. for "parquet" format options see <code>DataFrameWriter.parquet()</code>
     </td>
@@ -2175,7 +2175,7 @@ Since Spark 2.4, `foreach` is available in Scala, Java and Python.
 <div class="codetabs">
 <div data-lang="scala"  markdown="1">
 
-In Scala, you have to extend the class `ForeachWriter` ([docs](api/scala/index.html#org.apache.spark.sql.ForeachWriter)).
+In Scala, you have to extend the class `ForeachWriter` ([docs](api/scala/org/apache/spark/sql/ForeachWriter.html)).
 
 {% highlight scala %}
 streamingDatasetOfString.writeStream.foreach(
@@ -2564,7 +2564,7 @@ lastProgress(query)       # the most recent progress update of this streaming qu
 </div>
 
 You can start any number of queries in a single SparkSession. They will all be running concurrently sharing the cluster resources. You can use `sparkSession.streams()` to get the `StreamingQueryManager`
-([Scala](api/scala/index.html#org.apache.spark.sql.streaming.StreamingQueryManager)/[Java](api/java/org/apache/spark/sql/streaming/StreamingQueryManager.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.streaming.StreamingQueryManager) docs)
+([Scala](api/scala/org/apache/spark/sql/streaming/StreamingQueryManager.html)/[Java](api/java/org/apache/spark/sql/streaming/StreamingQueryManager.html)/[Python](api/python/pyspark.sql.html#pyspark.sql.streaming.StreamingQueryManager) docs)
 that can be used to manage the currently active queries.
 
 <div class="codetabs">
@@ -2624,7 +2624,7 @@ There are multiple ways to monitor active streaming queries. You can either push
 You can directly get the current status and metrics of an active query using 
 `streamingQuery.lastProgress()` and `streamingQuery.status()`. 
 `lastProgress()` returns a `StreamingQueryProgress` object 
-in [Scala](api/scala/index.html#org.apache.spark.sql.streaming.StreamingQueryProgress) 
+in [Scala](api/scala/org/apache/spark/sql/streaming/StreamingQueryProgress.html) 
 and [Java](api/java/org/apache/spark/sql/streaming/StreamingQueryProgress.html)
 and a dictionary with the same fields in Python. It has all the information about
 the progress made in the last trigger of the stream - what data was processed, 
@@ -2632,7 +2632,7 @@ what were the processing rates, latencies, etc. There is also
 `streamingQuery.recentProgress` which returns an array of last few progresses.  
 
 In addition, `streamingQuery.status()` returns a `StreamingQueryStatus` object 
-in [Scala](api/scala/index.html#org.apache.spark.sql.streaming.StreamingQueryStatus) 
+in [Scala](api/scala/org/apache/spark/sql/streaming/StreamingQueryStatus.html) 
 and [Java](api/java/org/apache/spark/sql/streaming/StreamingQueryStatus.html)
 and a dictionary with the same fields in Python. It gives information about
 what the query is immediately doing - is a trigger active, is data being processed, etc.
@@ -2853,7 +2853,7 @@ Will print something like the following.
 
 You can also asynchronously monitor all queries associated with a
 `SparkSession` by attaching a `StreamingQueryListener`
-([Scala](api/scala/index.html#org.apache.spark.sql.streaming.StreamingQueryListener)/[Java](api/java/org/apache/spark/sql/streaming/StreamingQueryListener.html) docs).
+([Scala](api/scala/org/apache/spark/sql/streaming/StreamingQueryListener.html)/[Java](api/java/org/apache/spark/sql/streaming/StreamingQueryListener.html) docs).
 Once you attach your custom `StreamingQueryListener` object with
 `sparkSession.streams.attachListener()`, you will get callbacks when a query is started and
 stopped and when there is progress made in an active query. Here is an example,
diff --git a/docs/tuning.md b/docs/tuning.md
index 1faf7cfe0d..8e29e5d2e9 100644
--- a/docs/tuning.md
+++ b/docs/tuning.md
@@ -260,7 +260,7 @@ enough. Spark automatically sets the number of "map" tasks to run on each file a
 (though you can control it through optional parameters to `SparkContext.textFile`, etc), and for
 distributed "reduce" operations, such as `groupByKey` and `reduceByKey`, it uses the largest
 parent RDD's number of partitions. You can pass the level of parallelism as a second argument
-(see the [`spark.PairRDDFunctions`](api/scala/index.html#org.apache.spark.rdd.PairRDDFunctions) documentation),
+(see the [`spark.PairRDDFunctions`](api/scala/org/apache/spark/rdd/PairRDDFunctions.html) documentation),
 or set the config property `spark.default.parallelism` to change the default.
 In general, we recommend 2-3 tasks per CPU core in your cluster.