[FIX][DOC] Fix broken links in ml-guide.md

and some minor changes in ScalaDoc.

Author: Xiangrui Meng <meng@databricks.com>

Closes #3601 from mengxr/SPARK-4575-fix and squashes the following commits:

c559768 [Xiangrui Meng] minor code update
ce94da8 [Xiangrui Meng] Java Bean -> JavaBean
0b5c182 [Xiangrui Meng] fix links in ml-guide
[SPARK-4683][SQL] Add a beeline.cmd to run on Windows

Tested locally with a Win7 VM. Connected to a Spark SQL Thrift server instance running on Mac OS X with the following command line:

```
bin\beeline.cmd -u jdbc:hive2://10.0.2.2:10000 -n lian
```

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Author: Cheng Lian <lian@databricks.com>

Closes #3599 from liancheng/beeline.cmd and squashes the following commits:

79092e7 [Cheng Lian] Windows script for BeeLine
[SPARK-4253] Ignore spark.driver.host in yarn-cluster and standalone-cluster modes

In yarn-cluster and standalone-cluster modes, we don't know where driver will run until it is launched.  If the `spark.driver.host` property is set on the submitting machine and propagated to the driver through SparkConf then this will lead to errors when the driver launches.

This patch fixes this issue by dropping the `spark.driver.host` property in SparkSubmit when running in a cluster deploy mode.

Author: WangTaoTheTonic <barneystinson@aliyun.com>
Author: WangTao <barneystinson@aliyun.com>

Closes #3112 from WangTaoTheTonic/SPARK4253 and squashes the following commits:

ed1a25c [WangTaoTheTonic] revert unrelated formatting issue
02c4e49 [WangTao] add comment
32a3f3f [WangTaoTheTonic] ingore it in SparkSubmit instead of SparkContext
667cf24 [WangTaoTheTonic] document fix
ff8d5f7 [WangTaoTheTonic] also ignore it in standalone cluster mode
2286e6b [WangTao] ignore spark.driver.host in yarn-cluster mode
[HOTFIX] Fixing two issues with the release script.

1. The version replacement was still producing some false changes.
2. Uploads to the staging repo specifically.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #3608 from pwendell/release-script and squashes the following commits:

3c63294 [Patrick Wendell] Fixing two issues with the release script:
[SPARK-4745] Fix get_existing_cluster() function with multiple security groups

The current get_existing_cluster() function would only find an instance belonged to a cluster if the instance's security groups == cluster_name + "-master" (or "-slaves"). This fix allows for multiple security groups by checking if the cluster_name + "-master" security group is in the list of groups for a particular instance.

Author: alexdebrie <alexdebrie1@gmail.com>

Closes #3596 from alexdebrie/master and squashes the following commits:

9d51232 [alexdebrie] Fix get_existing_cluster() function with multiple security groups
[SPARK-4459] Change groupBy type parameter from K to U

Please see https://issues.apache.org/jira/browse/SPARK-4459

Author: Saldanha <saldaal1@phusca-l24858.wlan.na.novartis.net>

Closes #3327 from alokito/master and squashes the following commits:

54b1095 [Saldanha] [SPARK-4459] changed type parameter for keyBy from K to U
d5f73c3 [Saldanha] [SPARK-4459] added keyBy test
316ad77 [Saldanha] SPARK-4459 changed type parameter for groupBy from K to U.
62ddd4b [Saldanha] SPARK-4459 added failing unit test
[SPARK-4652][DOCS] Add docs about spark-git-repo option

There might be some cases when WIPS spark version need to be run
on EC2 cluster. In order to setup this type of cluster more easily,
add --spark-git-repo option description to ec2 documentation.

Author: lewuathe <lewuathe@me.com>
Author: Josh Rosen <joshrosen@databricks.com>

Closes #3513 from Lewuathe/doc-for-development-spark-cluster and squashes the following commits:

6dae8ee [lewuathe] Wrap consistent with other descriptions
cfaf9be [lewuathe] Add docs about spark-git-repo option

(Editing / cleanup by Josh Rosen)
[SPARK-4397] Move object RDD to the front of RDD.scala.

I ran into multiple cases that SBT/Scala compiler was confused by the implicits in continuous compilation mode. Adding explicit return types fixes the problem.

Author: Reynold Xin <rxin@databricks.com>

Closes #3580 from rxin/rdd-implicit and squashes the following commits:

ee32fcd [Reynold Xin] Move object RDD to the end of the file.
b8562c9 [Reynold Xin] Merge branch 'master' of github.com:apache/spark into rdd-implicit
d4e9f85 [Reynold Xin] Code review.
a836a37 [Reynold Xin] Move object RDD to the front of RDD.scala.
[SPARK-4421] Wrong link in spark-standalone.html

Modified the link of building Spark.

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3279 from tsudukim/feature/SPARK-4421 and squashes the following commits:

56e31c1 [Masayoshi TSUZUKI] Modified the link of building Spark.
Fix typo in Spark SQL docs.

Author: Andy Konwinski <andykonwinski@gmail.com>

Closes #3611 from andyk/patch-3 and squashes the following commits:

7bab333 [Andy Konwinski] Fix typo in Spark SQL docs.
[SPARK-4464] Description about configuration options need to be modified in docs.

Added description about -h and -host.
Modified description about -i and -ip which are now deprecated.
Added description about --properties-file.

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3329 from tsudukim/feature/SPARK-4464 and squashes the following commits:

6c07caf [Masayoshi TSUZUKI] [SPARK-4464] Description about configuration options need to be modified in docs.
Revert "[HOT FIX] [YARN] Check whether `/lib` exists before listing its files"

This reverts commit 90ec643e9af4c8bbb9000edca08c07afb17939c7.
Revert "SPARK-2624 add datanucleus jars to the container in yarn-cluster"

This reverts commit a975dc32799bb8a14f9e1c76defaaa7cfbaf8b53.
[SPARK-4753][SQL] Use catalyst for partition pruning in newParquet.

Author: Michael Armbrust <michael@databricks.com>

Closes #3613 from marmbrus/parquetPartitionPruning and squashes the following commits:

4f138f8 [Michael Armbrust] Use catalyst for partition pruning in newParquet.
[SPARK-4761][SQL] Enables Kryo by default in Spark SQL Thrift server

Enables Kryo and disables reference tracking by default in Spark SQL Thrift server. Configurations explicitly defined by users in `spark-defaults.conf` are respected (the Thrift server is started by `spark-submit`, which handles configuration properties properly).

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Author: Cheng Lian <lian@databricks.com>

Closes #3621 from liancheng/kryo-by-default and squashes the following commits:

70c2775 [Cheng Lian] Enables Kryo by default in Spark SQL Thrift server
[SPARK-4005][CORE] handle message replies in receive instead of in the individual private methods

In BlockManagermasterActor, when handling message type UpdateBlockInfo, the message replies is in handled in individual private methods, should handle it in receive of Akka.

Author: Zhang, Liye <liye.zhang@intel.com>

Closes #2853 from liyezhang556520/akkaRecv and squashes the following commits:

9b06f0a [Zhang, Liye] remove the unreachable code
bf518cd [Zhang, Liye] change the indent
242166b [Zhang, Liye] modified accroding to the comments
d4b929b [Zhang, Liye] [SPARK-4005][CORE] handle message replies in receive instead of in the individual private methods
Streaming doc : do you mean inadvertently?

Author: CrazyJvm <crazyjvm@gmail.com>

Closes #3620 from CrazyJvm/streaming-foreachRDD and squashes the following commits:

b72886b [CrazyJvm] do you mean inadvertently?
[SPARK-3623][GraphX] GraphX should support the checkpoint operation

Author: GuoQiang Li <witgo@qq.com>

Closes #2631 from witgo/SPARK-3623 and squashes the following commits:

a70c500 [GuoQiang Li] Remove java related
4d1e249 [GuoQiang Li] Add comments
e682724 [GuoQiang Li] Graph should support the checkpoint operation
[SPARK-4646] Replace Scala.util.Sorting.quickSort with Sorter(TimSort) in Spark

This patch just replaces a native quick sorter with Sorter(TimSort) in Spark.
It could get performance gains by ~8% in my quick experiments.

Author: Takeshi Yamamuro <linguin.m.s@gmail.com>

Closes #3507 from maropu/TimSortInEdgePartitionBuilderSpike and squashes the following commits:

8d4e5d2 [Takeshi Yamamuro] Remove a wildcard import
3527e00 [Takeshi Yamamuro] Replace Scala.util.Sorting.quickSort with Sorter(TimSort) in Spark
[SPARK-4620] Add unpersist in Graph and GraphImpl

Add an IF to uncache both vertices and edges of Graph/GraphImpl.
This IF is useful when iterative graph operations build a new graph in each iteration, and the vertices and edges of previous iterations are no longer needed for following iterations.

Author: Takeshi Yamamuro <linguin.m.s@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Ankur Dave <ankurdave@gmail.com>

Closes #3476 from maropu/UnpersistInGraphSpike and squashes the following commits:

77a006a [Takeshi Yamamuro] Add unpersist in Graph and GraphImpl