This is a fairly large PR to clean up and update the docs for 1.0. The major changes are:

* A unified programming guide for all languages replaces language-specific ones and shows language-specific info in tabs
* New programming guide sections on key-value pairs, unit testing, input formats beyond text, migrating from 0.9, and passing functions to Spark
* Spark-submit guide moved to a separate page and expanded slightly
* Various cleanups of the menu system, security docs, and others
* Updated look of title bar to differentiate the docs from previous Spark versions

You can find the updated docs at http://people.apache.org/~matei/1.0-docs/_site/ and in particular http://people.apache.org/~matei/1.0-docs/_site/programming-guide.html.

Author: Matei Zaharia <matei@databricks.com>

Closes #896 from mateiz/1.0-docs and squashes the following commits:

03e6853 [Matei Zaharia] Some tweaks to configuration and YARN docs
0779508 [Matei Zaharia] tweak
ef671d4 [Matei Zaharia] Keep frames in JavaDoc links, and other small tweaks
1bf4112 [Matei Zaharia] Review comments
4414f88 [Matei Zaharia] tweaks
d04e979 [Matei Zaharia] Fix some old links to Java guide
a34ed33 [Matei Zaharia] tweak
541bb3b [Matei Zaharia] miscellaneous changes
fcefdec [Matei Zaharia] Moved submitting apps to separate doc
61d72b4 [Matei Zaharia] stuff
181f217 [Matei Zaharia] migration guide, remove old language guides
e11a0da [Matei Zaharia] Add more API functions
6a030a9 [Matei Zaharia] tweaks
8db0ae3 [Matei Zaharia] Added key-value pairs section
318d2c9 [Matei Zaharia] tweaks
1c81477 [Matei Zaharia] New section on basics and function syntax
e38f559 [Matei Zaharia] Actually added programming guide to Git
a33d6fe [Matei Zaharia] First pass at updating programming guide to support all languages, plus other tweaks throughout
3b6a876 [Matei Zaharia] More CSS tweaks
01ec8bf [Matei Zaharia] More CSS tweaks
e6d252e [Matei Zaharia] Change color of doc title bar to differentiate from 0.9.0

Author: Patrick Wendell <pwendell@gmail.com>

Closes #784 from pwendell/group-by-key and squashes the following commits:

9b4505f [Patrick Wendell] Small fix
6347924 [Patrick Wendell] Documentation: Encourage use of reduceByKey instead of groupByKey.

YARN
- SparkPi was updated to not take in master as an argument; we should update the docs to reflect that.
- The default YARN build guide should be in maven, not sbt.
- This PR also adds a paragraph on steps to debug a YARN application.

Standalone
- Emphasize spark-submit more. Right now it's one small paragraph preceding the legacy way of launching through `org.apache.spark.deploy.Client`.
- The way we set configurations / environment variables according to the old docs is outdated. This needs to reflect changes introduced by the Spark configuration changes we made.

In general, this PR also adds a little more documentation on the new spark-shell, spark-submit, spark-defaults.conf etc here and there.

Author: Andrew Or <andrewor14@gmail.com>

Closes #701 from andrewor14/yarn-docs and squashes the following commits:

e2c2312 [Andrew Or] Merge in changes in #752 (SPARK-1814)
25cfe7b [Andrew Or] Merge in the warning from SPARK-1753
a8c39c5 [Andrew Or] Minor changes
336bbd9 [Andrew Or] Tabs -> spaces
4d9d8f7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
041017a [Andrew Or] Abstract Spark submit documentation to cluster-overview.html
3cc0649 [Andrew Or] Detail how to set configurations + remove legacy instructions
5b7140a [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
85a51fc [Andrew Or] Update run-example, spark-shell, configuration etc.
c10e8c7 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
381fe32 [Andrew Or] Update docs for standalone mode
757c184 [Andrew Or] Add a note about the requirements for the debugging trick
f8ca990 [Andrew Or] Merge branch 'master' of github.com:apache/spark into yarn-docs
924f04c [Andrew Or] Revert addition of --deploy-mode
d5fe17b [Andrew Or] Update the YARN docs

... with regards to saved map output. Wording taken partially from Matei Zaharia's email to the Spark user list. http://apache-spark-user-list.1001560.n3.nabble.com/performance-improvement-on-second-operation-without-caching-td5227.html

Author: Ethan Jewett <esjewett@gmail.com>

Closes #668 from esjewett/Doc-update and squashes the following commits:

11793ce [Ethan Jewett] Update based on feedback
171e670 [Ethan Jewett] Clarify Scala programming guide on caching ...

While play-testing the Scala and Java code examples in the MLlib docs, I noticed a number of small compile errors, and some typos. This led to finding and fixing a few similar items in other docs.

Then in the course of building the site docs to check the result, I found a few small suggestions for the build instructions. I also found a few more formatting and markdown issues uncovered when I accidentally used maruku instead of kramdown.

Author: Sean Owen <sowen@cloudera.com>

Closes #653 from srowen/SPARK-1727 and squashes the following commits:

6e7c38a [Sean Owen] Final doc updates - one more compile error, and use of mean instead of sum and count
8f5e847 [Sean Owen] Fix markdown syntax issues that maruku flags, even though we use kramdown (but only those that do not affect kramdown's output)
99966a9 [Sean Owen] Update issue tracker URL in docs
23c9ac3 [Sean Owen] Add Scala Naive Bayes example, to use existing example data file (whose format needed a tweak)
8c81982 [Sean Owen] Fix small compile errors and typos across MLlib docs

This simplifies the shell a bunch and passes all arguments through to spark-submit.

There is a tiny incompatibility from 0.9.1 which is that you can't put `-c` _or_ `--cores`, only `--cores`. However, spark-submit will give a good error message in this case, I don't think many people used this, and it's a trivial change for users.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #542 from pwendell/spark-shell and squashes the following commits:

9eb3e6f [Patrick Wendell] Updating Spark docs
b552459 [Patrick Wendell] Andrew's feedback
97720fa [Patrick Wendell] Review feedback
aa2900b [Patrick Wendell] SPARK-1619 Launch spark-shell with spark-submit

I used the sbt-unidoc plugin (https://github.com/sbt/sbt-unidoc) to create a unified Scaladoc of our public packages, and generate Javadocs as well. One limitation is that I haven't found an easy way to exclude packages in the Javadoc; there is a SBT task that identifies Java sources to run javadoc on, but it's been very difficult to modify it from outside to change what is set in the unidoc package. Some SBT-savvy people should help with this. The Javadoc site also lacks package-level descriptions and things like that, so we may want to look into that. We may decide not to post these right now if it's too limited compared to the Scala one.

Example of the built doc site: http://people.csail.mit.edu/matei/spark-unified-docs/

Author: Matei Zaharia <matei@databricks.com>

This patch had conflicts when merged, resolved by
Committer: Patrick Wendell <pwendell@gmail.com>

Closes #457 from mateiz/better-docs and squashes the following commits:

a63d4a3 [Matei Zaharia] Skip Java/Scala API docs for Python package
5ea1f43 [Matei Zaharia] Fix links to Java classes in Java guide, fix some JS for scrolling to anchors on page load
f05abc0 [Matei Zaharia] Don't include java.lang package names
995e992 [Matei Zaharia] Skip internal packages and class names with $ in JavaDoc
a14a93c [Matei Zaharia] typo
76ce64d [Matei Zaharia] Add groups to Javadoc index page, and a first package-info.java
ed6f994 [Matei Zaharia] Generate JavaDoc as well, add titles, update doc site to use unified docs
acb993d [Matei Zaharia] Add Unidoc plugin for the projects we want Unidoced

Over time as we've added more deployment modes, this have gotten a bit unwieldy with user-facing configuration options in Spark. Going forward we'll advise all users to run `spark-submit` to launch applications. This is a WIP patch but it makes the following improvements:

1. Improved `spark-env.sh.template` which was missing a lot of things users now set in that file.
2. Removes the shipping of SPARK_CLASSPATH, SPARK_JAVA_OPTS, and SPARK_LIBRARY_PATH to the executors on the cluster. This was an ugly hack. Instead it introduces config variables spark.executor.extraJavaOpts, spark.executor.extraLibraryPath, and spark.executor.extraClassPath.
3. Adds ability to set these same variables for the driver using `spark-submit`.
4. Allows you to load system properties from a `spark-defaults.conf` file when running `spark-submit`. This will allow setting both SparkConf options and other system properties utilized by `spark-submit`.
5. Made `SPARK_LOCAL_IP` an environment variable rather than a SparkConf property. This is more consistent with it being set on each node.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #299 from pwendell/config-cleanup and squashes the following commits:

127f301 [Patrick Wendell] Improvements to testing
a006464 [Patrick Wendell] Moving properties file template.
b4b496c [Patrick Wendell] spark-defaults.properties -> spark-defaults.conf
0086939 [Patrick Wendell] Minor style fixes
af09e3e [Patrick Wendell] Mention config file in docs and clean-up docs
b16e6a2 [Patrick Wendell] Cleanup of spark-submit script and Scala quick start guide
af0adf7 [Patrick Wendell] Automatically add user jar
a56b125 [Patrick Wendell] Responses to Tom's review
d50c388 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into config-cleanup
a762901 [Patrick Wendell] Fixing test failures
ffa00fe [Patrick Wendell] Review feedback
fda0301 [Patrick Wendell] Note
308f1f6 [Patrick Wendell] Properly escape quotes and other clean-up for YARN
e83cd8f [Patrick Wendell] Changes to allow re-use of test applications
be42f35 [Patrick Wendell] Handle case where SPARK_HOME is not set
c2a2909 [Patrick Wendell] Test compile fixes
4ee6f9d [Patrick Wendell] Making YARN doc changes consistent
afc9ed8 [Patrick Wendell] Cleaning up line limits and two compile errors.
b08893b [Patrick Wendell] Additional improvements.
ace4ead [Patrick Wendell] Responses to review feedback.
b72d183 [Patrick Wendell] Review feedback for spark env file
46555c1 [Patrick Wendell] Review feedback and import clean-ups
437aed1 [Patrick Wendell] Small fix
761ebcd [Patrick Wendell] Library path and classpath for drivers
7cc70e4 [Patrick Wendell] Clean up terminology inside of spark-env script
5b0ba8e [Patrick Wendell] Don't ship executor envs
84cc5e5 [Patrick Wendell] Small clean-up
1f75238 [Patrick Wendell] SPARK_JAVA_OPTS --> SPARK_MASTER_OPTS for master settings
4982331 [Patrick Wendell] Remove SPARK_LIBRARY_PATH
6eaf7d0 [Patrick Wendell] executorJavaOpts
0faa3b6 [Patrick Wendell] Stash of adding config options in submit script and YARN
ac2d65e [Patrick Wendell] Change spark.local.dir -> SPARK_LOCAL_DIRS

"By default, this uses only 8 parallel tasks to do the grouping." is a big misleading. Please refer to https://github.com/apache/spark/pull/389

detail is as following code :

  def defaultPartitioner(rdd: RDD[_], others: RDD[_]*): Partitioner = {
    val bySize = (Seq(rdd) ++ others).sortBy(_.partitions.size).reverse
    for (r <- bySize if r.partitioner.isDefined) {
      return r.partitioner.get
    }
    if (rdd.context.conf.contains("spark.default.parallelism")) {
      new HashPartitioner(rdd.context.defaultParallelism)
    } else {
      new HashPartitioner(bySize.head.partitions.size)
    }
  }

Author: Chen Chao <crazyjvm@gmail.com>

Closes #403 from CrazyJvm/patch-4 and squashes the following commits:

42f6c9e [Chen Chao] fix format
829a995 [Chen Chao] fix format
1568336 [Chen Chao] misleading task number of groupByKey

This is the default mode for running spark-shell and pyspark, intended to allow users running spark for the first time to see the performance benefits of using multiple cores, while not breaking backwards compatibility for users who use "local" mode and expect exactly 1 core.

Author: Aaron Davidson <aaron@databricks.com>

Closes #182 from aarondav/110 and squashes the following commits:

a88294c [Aaron Davidson] Rebased changes for new spark-shell
a9f393e [Aaron Davidson] SPARK-1099: Introduce local[*] mode to infer number of cores

Move the PR#468 of apache-incubator-spark to the apache-spark
"Adding an option to persist Spark RDD blocks into Tachyon."

Author: Haoyuan Li <haoyuan@cs.berkeley.edu>
Author: RongGu <gurongwalker@gmail.com>

Closes #158 from RongGu/master and squashes the following commits:

72b7768 [Haoyuan Li] merge master
9f7fa1b [Haoyuan Li] fix code style
ae7834b [Haoyuan Li] minor cleanup
a8b3ec6 [Haoyuan Li] merge master branch
e0f4891 [Haoyuan Li] better check offheap.
55b5918 [RongGu] address matei's comment on the replication of offHeap storagelevel
7cd4600 [RongGu] remove some logic code for tachyonstore's replication
51149e7 [RongGu] address aaron's comment on returning value of the remove() function in tachyonstore
8adfcfa [RongGu] address arron's comment on inTachyonSize
120e48a [RongGu] changed the root-level dir name in Tachyon
5cc041c [Haoyuan Li] address aaron's comments
9b97935 [Haoyuan Li] address aaron's comments
d9a6438 [Haoyuan Li] fix for pspark
77d2703 [Haoyuan Li] change python api.git status
3dcace4 [Haoyuan Li] address matei's comments
91fa09d [Haoyuan Li] address patrick's comments
589eafe [Haoyuan Li] use TRY_CACHE instead of MUST_CACHE
64348b2 [Haoyuan Li] update conf docs.
ed73e19 [Haoyuan Li] Merge branch 'master' of github.com:RongGu/spark-1
619a9a8 [RongGu] set number of directories in TachyonStore back to 64; added a TODO tag for duplicated code from the DiskStore
be79d77 [RongGu] find a way to clean up some unnecessay metods and classed to make the code simpler
49cc724 [Haoyuan Li] update docs with off_headp option
4572f9f [RongGu] reserving the old apply function API of StorageLevel
04301d3 [RongGu] rename StorageLevel.TACHYON to Storage.OFF_HEAP
c9aeabf [RongGu] rename the StorgeLevel.TACHYON as StorageLevel.OFF_HEAP
76805aa [RongGu] unifies the config properties name prefix; add the configs into docs/configuration.md
e700d9c [RongGu] add the SparkTachyonHdfsLR example and some comments
fd84156 [RongGu] use randomUUID to generate sparkapp directory name on tachyon;minor code style fix
939e467 [Haoyuan Li] 0.4.1-thrift from maven central
86a2eab [Haoyuan Li] tachyon 0.4.1-thrift is in the staging repo. but jenkins failed to download it. temporarily revert it back to 0.4.1
16c5798 [RongGu] make the dependency on tachyon as tachyon-0.4.1-thrift
eacb2e8 [RongGu] Merge branch 'master' of https://github.com/RongGu/spark-1
bbeb4de [RongGu] fix the JsonProtocolSuite test failure problem
6adb58f [RongGu] Merge branch 'master' of https://github.com/RongGu/spark-1
d827250 [RongGu] fix JsonProtocolSuie test failure
716e93b [Haoyuan Li] revert the version
ca14469 [Haoyuan Li] bump tachyon version to 0.4.1-thrift
2825a13 [RongGu] up-merging to the current master branch of the apache spark
6a22c1a [Haoyuan Li] fix scalastyle
8968b67 [Haoyuan Li] exclude more libraries from tachyon dependency to be the same as referencing tachyon-client.
77be7e8 [RongGu] address mateiz's comment about the temp folder name problem. The implementation followed mateiz's advice.
1dcadf9 [Haoyuan Li] typo
bf278fa [Haoyuan Li] fix python tests
e82909c [Haoyuan Li] minor cleanup
776a56c [Haoyuan Li] address patrick's and ali's comments from the previous PR
8859371 [Haoyuan Li] various minor fixes and clean up
e3ddbba [Haoyuan Li] add doc to use Tachyon cache mode.
fcaeab2 [Haoyuan Li] address Aaron's comment
e554b1e [Haoyuan Li] add python code
47304b3 [Haoyuan Li] make tachyonStore in BlockMananger lazy val; add more comments StorageLevels.
dc8ef24 [Haoyuan Li] add old storelevel constructor
e01a271 [Haoyuan Li] update tachyon 0.4.1
8011a96 [RongGu] fix a brought-in mistake in StorageLevel
70ca182 [RongGu] a bit change in comment
556978b [RongGu] fix the scalastyle errors
791189b [RongGu] "Adding an option to persist Spark RDD blocks into Tachyon." move the PR#468 of apache-incubator-spark to the apache-spark

Author: Reynold Xin <rxin@apache.org>

Closes #2 from rxin/docs and squashes the following commits:

08bbd5f [Reynold Xin] Removed reference to incubation in Spark user docs.

The current doc hints spark doesn't support accumulators of type `Long`, which is wrong.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1117

Author: Xiangrui Meng <meng@databricks.com>

Closes #631 from mengxr/acc and squashes the following commits:

45ecd25 [Xiangrui Meng] update accumulator docs

https://spark-project.atlassian.net/browse/SPARK-1105

fix site scala version error

Author: CodingCat <zhunansjtu@gmail.com>

Closes #618 from CodingCat/doc_version and squashes the following commits:

39bb8aa [CodingCat] more fixes
65bedb0 [CodingCat] fix site scala version error in doc

Also, replace the last reference to it in the docs.

This fixes SPARK-1026.

This reverts commit 79b20e4d, reversing
changes made to 7375047d.

val => var

Also changed uses of "job" terminology to "application" when they
referred to an entire Spark program, to avoid confusion.

* RDD, *RDDFunctions -> org.apache.spark.rdd
* Utils, ClosureCleaner, SizeEstimator -> org.apache.spark.util
* JavaSerializer, KryoSerializer -> org.apache.spark.serializer

This commit makes Spark invocation saner by using an assembly JAR to
find all of Spark's dependencies instead of adding all the JARs in
lib_managed. It also packages the examples into an assembly and uses
that as SPARK_EXAMPLES_JAR. Finally, it replaces the old "run" script
with two better-named scripts: "run-examples" for examples, and
"spark-class" for Spark internal classes (e.g. REPL, master, etc). This
is also designed to minimize the confusion people have in trying to use
"run" to run their own classes; it's not meant to do that, but now at
least if they look at it, they can modify run-examples to do a decent
job for them.

As part of this, Bagel's examples are also now properly moved to the
examples package instead of bagel.

Also warns if spark.cleaner.ttl is not set in the version where you pass
your own SparkContext.

ordering, so the reduce function must also be commutative.

Made StorageLevel constructor private, and added StorageLevels.create() to the Java API. Updates scala and java programming guides.