Docs: move HA subsections to a deeper indentation level

Makes the table of contents read better

Author: Andrew Ash <andrew@andrewash.com>

Closes #2402 from ash211/docs/better-indentation and squashes the following commits:

ea0e130 [Andrew Ash] Move HA subsections to a deeper indentation level
[SPARK-3534] Fix expansion of testing arguments to sbt

Testing arguments to `sbt` need to be passed as an array, not a single, long string.

Fixes a bug introduced in #2420.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2437 from nchammas/selective-testing and squashes the following commits:

a9f9c1c [Nicholas Chammas] fix printing of sbt test arguments
cf57cbf [Nicholas Chammas] fix sbt test arguments
e33b978 [Nicholas Chammas] Merge pull request #2 from apache/master
0b47ca4 [Nicholas Chammas] Merge branch 'master' of github.com:nchammas/spark
8051486 [Nicholas Chammas] Merge pull request #1 from apache/master
03180a4 [Nicholas Chammas] Merge branch 'master' of github.com:nchammas/spark
d4c5f43 [Nicholas Chammas] Merge pull request #6 from apache/master
[SPARK-3571] Spark standalone cluster mode doesn't work.

I think, this issue is caused by #1106

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #2436 from sarutak/SPARK-3571 and squashes the following commits:

7a4deea [Kousuke Saruta] Modified Master.scala to use numWorkersVisited and numWorkersAlive instead of stopPos
4e51e35 [Kousuke Saruta] Modified Master to prevent from 0 divide
4817ecd [Kousuke Saruta] Brushed up previous change
71e84b6 [Kousuke Saruta] Modified Master to enable schedule normally
[SPARK-3564][WebUI] Display App ID on HistoryPage

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #2424 from sarutak/display-appid-on-webui and squashes the following commits:

417fe90 [Kousuke Saruta] Added "App ID column" to HistoryPage
[SPARK-3567] appId field in SparkDeploySchedulerBackend should be volatile

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #2428 from sarutak/appid-volatile-modification and squashes the following commits:

c7d890d [Kousuke Saruta] Added volatile modifier to appId field in SparkDeploySchedulerBackend
[SPARK-3565]Fix configuration item not consistent with document

https://issues.apache.org/jira/browse/SPARK-3565

"spark.ports.maxRetries" should be "spark.port.maxRetries". Make the configuration keys in document and code consistent.

Author: WangTaoTheTonic <barneystinson@aliyun.com>

Closes #2427 from WangTaoTheTonic/fixPortRetries and squashes the following commits:

c178813 [WangTaoTheTonic] Use blank lines trigger Jenkins
646f3fe [WangTaoTheTonic] also in SparkBuild.scala
3700dba [WangTaoTheTonic] Fix configuration item not consistent with document
[SPARK-3534] Add hive-thriftserver to SQL tests

Addresses the problem pointed out in [this comment](https://github.com/apache/spark/pull/2441#issuecomment-55990116).

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2442 from nchammas/patch-1 and squashes the following commits:

7e68b60 [Nicholas Chammas] [SPARK-3534] Add hive-thriftserver to SQL tests
[Minor] rat exclude dependency-reduced-pom.xml

Author: GuoQiang Li <witgo@qq.com>

Closes #2326 from witgo/rat-excludes and squashes the following commits:

860904e [GuoQiang Li] rat exclude dependency-reduced-pom.xml
[SPARK-3547]Using a special exit code instead of 1 to represent ClassNotFoundExcepti...

...on

As improvement of https://github.com/apache/spark/pull/1944, we should use more special exit code to represent ClassNotFoundException.

Author: WangTaoTheTonic <barneystinson@aliyun.com>

Closes #2421 from WangTaoTheTonic/classnotfoundExitCode and squashes the following commits:

645a22a [WangTaoTheTonic] Serveral typos to trigger Jenkins
d6ae559 [WangTaoTheTonic] use 101 instead
a2d6465 [WangTaoTheTonic] use 127 instead
fbb232f [WangTaoTheTonic] Using a special exit code instead of 1 to represent ClassNotFoundException
SPARK-3579 Jekyll doc generation is different across environments.

This patch makes some small changes to fix this problem:
1. We document specific versions of Jekyll/Kramdown to use that match
   those used when building the upstream docs.
2. We add a configuration for a property that for some reason varies across
   packages of Jekyll/Kramdown even with the same version.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #2443 from pwendell/jekyll and squashes the following commits:

54ee2ab [Patrick Wendell] SPARK-3579 Jekyll doc generation is different across environments.
[SPARK-3566] [BUILD] .gitignore and .rat-excludes should consider Windows cmd file and Emacs' backup files

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #2426 from sarutak/emacs-metafiles-ignore and squashes the following commits:

a306020 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into emacs-metafiles-ignore
6a0a5eb [Kousuke Saruta] Added cmd file entry to .rat-excludes and .gitignore
897da63 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into emacs-metafiles-ignore
8cade06 [Kousuke Saruta] Modified .gitignore to ignore emacs lock file and backup file
[SPARK-3589][Minor]remove redundant code

https://issues.apache.org/jira/browse/SPARK-3589

"export CLASSPATH" in spark-class is redundant since same variable is exported before.
We could reuse defined value "isYarnCluster" in SparkSubmit.scala.

Author: WangTaoTheTonic <barneystinson@aliyun.com>

Closes #2445 from WangTaoTheTonic/removeRedundant and squashes the following commits:

6fb6872 [WangTaoTheTonic] remove redundant code
[SPARK-3560] Fixed setting spark.jars system property in yarn-cluster mode

Author: Victsm <victor.nju@gmail.com>
Author: Min Shen <mshen@linkedin.com>

Closes #2449 from Victsm/SPARK-3560 and squashes the following commits:

918405a [Victsm] Removed the additional space
4502a2a [Min Shen] [SPARK-3560] Fixed setting spark.jars system property in yarn-cluster mode.

(cherry picked from commit 832dff64ddb1240a4c8e22fcdc0e993cc8c808de)
Signed-off-by: Andrew Or <andrewor14@gmail.com>
[Minor Hot Fix] Move a line in SparkSubmit to the right place

This was introduced in #2449

Author: Andrew Or <andrewor14@gmail.com>

Closes #2452 from andrewor14/standalone-hot-fix and squashes the following commits:

d5190ca [Andrew Or] Put that line in the right place
[SPARK-3554] [PySpark] use broadcast automatically for large closure

Py4j can not handle large string efficiently, so we should use broadcast for large closure automatically. (Broadcast use local filesystem to pass through data).

Author: Davies Liu <davies.liu@gmail.com>

Closes #2417 from davies/command and squashes the following commits:

fbf4e97 [Davies Liu] bugfix
aefd508 [Davies Liu] use broadcast automatically for large closure
[SPARK-3418] Sparse Matrix support (CCS) and additional native BLAS operations added

Local `SparseMatrix` support added in Compressed Column Storage (CCS) format in addition to Level-2 and Level-3 BLAS operations such as dgemv and dgemm respectively.

BLAS doesn't support  sparse matrix operations, therefore support for `SparseMatrix`-`DenseMatrix` multiplication and `SparseMatrix`-`DenseVector` implementations have been added. I will post performance comparisons in the comments momentarily.

Author: Burak <brkyvz@gmail.com>

Closes #2294 from brkyvz/SPARK-3418 and squashes the following commits:

88814ed [Burak] Hopefully fixed MiMa this time
47e49d5 [Burak] really fixed MiMa issue
f0bae57 [Burak] [SPARK-3418] Fixed MiMa compatibility issues (excluded from check)
4b7dbec [Burak] 9/17 comments addressed
7af2f83 [Burak] sealed traits Vector and Matrix
d3a8a16 [Burak] [SPARK-3418] Squashed missing alpha bug.
421045f [Burak] [SPARK-3418] New code review comments addressed
f35a161 [Burak] [SPARK-3418] Code review comments addressed and multiplication further optimized
2508577 [Burak] [SPARK-3418] Fixed one more style issue
d16e8a0 [Burak] [SPARK-3418] Fixed style issues and added documentation for methods
204a3f7 [Burak] [SPARK-3418] Fixed failing Matrix unit test
6025297 [Burak] [SPARK-3418] Fixed Scala-style errors
dc7be71 [Burak] [SPARK-3418][MLlib] Matrix unit tests expanded with indexing and updating
d2d5851 [Burak] [SPARK-3418][MLlib] Sparse Matrix support and additional native BLAS operations added
[SPARK-2062][GraphX] VertexRDD.apply does not use the mergeFunc

VertexRDD.apply had a bug where it ignored the merge function for
duplicate vertices and instead used whichever vertex attribute occurred
first. This commit fixes the bug by passing the merge function through
to ShippableVertexPartition.apply, which merges any duplicates using the
merge function and then fills in missing vertices using the specified
default vertex attribute. This commit also adds a unit test for
VertexRDD.apply.

Author: Larry Xiao <xiaodi@sjtu.edu.cn>
Author: Blie Arkansol <xiaodi@sjtu.edu.cn>
Author: Ankur Dave <ankurdave@gmail.com>

Closes #1903 from larryxiao/2062 and squashes the following commits:

625aa9d [Blie Arkansol] Merge pull request #1 from ankurdave/SPARK-2062
476770b [Ankur Dave] ShippableVertexPartition.initFrom: Don't run mergeFunc on default values
614059f [Larry Xiao] doc update: note about the default null value vertices construction
dfdb3c9 [Larry Xiao] minor fix
1c70366 [Larry Xiao] scalastyle check: wrap line, parameter list indent 4 spaces
e4ca697 [Larry Xiao] [TEST] VertexRDD.apply mergeFunc
6a35ea8 [Larry Xiao] [TEST] VertexRDD.apply mergeFunc
4fbc29c [Blie Arkansol] undo unnecessary change
efae765 [Larry Xiao] fix mistakes: should be able to call with or without mergeFunc
b2422f9 [Larry Xiao] Merge branch '2062' of github.com:larryxiao/spark into 2062
52dc7f7 [Larry Xiao] pass mergeFunc to VertexPartitionBase, where merge is handled
581e9ee [Larry Xiao] TODO: VertexRDDSuite
20d80a3 [Larry Xiao] [SPARK-2062][GraphX] VertexRDD.apply does not use the mergeFunc
MAINTENANCE: Automated closing of pull requests.

This commit exists to close the following pull requests on Github:

Closes #726 (close requested by 'pwendell')
Closes #151 (close requested by 'pwendell')
Merge pull request #3 from apache/master

merge upstream changes