Organize configuration docs

This PR improves and organizes the config option page
and makes a few other changes to config docs. See a preview here:
http://people.apache.org/~pwendell/config-improvements/configuration.html

The biggest changes are:
1. The configs for the standalone master/workers were moved to the
standalone page and out of the general config doc.
2. SPARK_LOCAL_DIRS was missing from the standalone docs.
3. Expanded discussion of injecting configs with spark-submit, including an
example.
4. Config options were organized into the following categories:
- Runtime Environment
- Shuffle Behavior
- Spark UI
- Compression and Serialization
- Execution Behavior
- Networking
- Scheduling
- Security
- Spark Streaming

Author: Patrick Wendell <pwendell@gmail.com>

Closes #880 from pwendell/config-cleanup and squashes the following commits:

93f56c3 [Patrick Wendell] Feedback from Matei
6f66efc [Patrick Wendell] More feedback
16ae776 [Patrick Wendell] Adding back header section
d9c264f [Patrick Wendell] Small fix
e0c1728 [Patrick Wendell] Response to Matei's review
27d57db [Patrick Wendell] Reverting changes to index.html (covered in #896)
e230ef9 [Patrick Wendell] Merge remote-tracking branch 'apache/master' into config-cleanup
a374369 [Patrick Wendell] Line wrapping fixes
fdff7fc [Patrick Wendell] Merge remote-tracking branch 'apache/master' into config-cleanup
3289ea4 [Patrick Wendell] Pulling in changes from #856
106ee31 [Patrick Wendell] Small link fix
f7e79bc [Patrick Wendell] Re-organizing config options.
54b184d [Patrick Wendell] Adding standalone configs to the standalone page
592e94a [Patrick Wendell] Stash
29b5446 [Patrick Wendell] Better discussion of spark-submit in configuration docs
2d719ef [Patrick Wendell] Small fix
4af9e07 [Patrick Wendell] Adding SPARK_LOCAL_DIRS docs
204b248 [Patrick Wendell] Small fixes
Spark 1916

The changes could be ported back to 0.9 as well.
Changing in.read to in.readFully to read the whole input stream rather than the first 1020 bytes.
This should ok considering that Flume caps the body size to 32K by default.

Author: David Lemieux <david.lemieux@radialpoint.com>

Closes #865 from lemieud/SPARK-1916 and squashes the following commits:

a265673 [David Lemieux] Updated SparkFlumeEvent to read the whole stream rather than the first X bytes.
(cherry picked from commit 0b769b73fb7ae314325857138a2d3138ed157908)

Signed-off-by: Patrick Wendell <pwendell@gmail.com>
[SPARK-1712]: TaskDescription instance is too big causes Spark to hang

Author: witgo <witgo@qq.com>

Closes #694 from witgo/SPARK-1712_new and squashes the following commits:

0f52483 [witgo] review commit
83ce29b [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
52e6752 [witgo] reset test SparkContext
63636b6 [witgo] review commit
44a59ee [witgo] review commit
3b6d48c [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
926bd6a [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
9a5cfad [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
03cc562 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
b0930b0 [witgo] review commit
b1174bd [witgo] merge master
f76679b [witgo] merge master
689495d [witgo] fix scala style bug
1d35c3c [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
062c182 [witgo] fix small bug for code style
0a428cf [witgo] add unit tests
158b2dc [witgo] review commit
4afe71d [witgo] review commit
9e4ffa7 [witgo] review commit
1d35c7d [witgo] fix hang
7965580 [witgo] fix Statement order
0e29eac [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
3ea1ca1 [witgo] remove duplicate serialize
743a7ad [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
86e2048 [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1712_new
2a89adc [witgo] SPARK-1712: TaskDescription instance is too big causes Spark to hang
Added doctest and method description in context.py

Added doctest for method textFile and description for methods _initialize_context and _ensure_initialized in context.py

Author: Jyotiska NK <jyotiska123@gmail.com>

Closes #187 from jyotiska/pyspark_context and squashes the following commits:

356f945 [Jyotiska NK] Added doctest for textFile method in context.py
5b23686 [Jyotiska NK] Updated context.py with method descriptions
SPARK-1935: Explicitly add commons-codec 1.5 as a dependency.

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #889 from yhuai/SPARK-1935 and squashes the following commits:

7d50ef1 [Yin Huai] Explicitly add commons-codec 1.5 as a dependency.
[SPARK-1368][SQL] Optimized HiveTableScan

JIRA issue: [SPARK-1368](https://issues.apache.org/jira/browse/SPARK-1368)

This PR introduces two major updates:

- Replaced FP style code with `while` loop and reusable `GenericMutableRow` object in critical path of `HiveTableScan`.
- Using `ColumnProjectionUtils` to help optimizing RCFile and ORC column pruning.

My quick micro benchmark suggests these two optimizations made the optimized version 2x and 2.5x faster when scanning CSV table and RCFile table respectively:

```
Original:

[info] CSV: 27676 ms, RCFile: 26415 ms
[info] CSV: 27703 ms, RCFile: 26029 ms
[info] CSV: 27511 ms, RCFile: 25962 ms

Optimized:

[info] CSV: 13820 ms, RCFile: 10402 ms
[info] CSV: 14158 ms, RCFile: 10691 ms
[info] CSV: 13606 ms, RCFile: 10346 ms
```

The micro benchmark loads a 609MB CVS file (structurally similar to the `src` test table) into a normal Hive table with `LazySimpleSerDe` and a RCFile table, then scans these tables respectively.

Preparation code:

```scala
package org.apache.spark.examples.sql.hive

import org.apache.spark.sql.hive.LocalHiveContext
import org.apache.spark.{SparkConf, SparkContext}

object HiveTableScanPrepare extends App {
  val sparkContext = new SparkContext(
    new SparkConf()
      .setMaster("local")
      .setAppName(getClass.getSimpleName.stripSuffix("$")))

  val hiveContext = new LocalHiveContext(sparkContext)

  import hiveContext._

  hql("drop table scan_csv")
  hql("drop table scan_rcfile")

  hql("""create table scan_csv (key int, value string)
        |  row format serde 'org.apache.hadoop.hive.serde2.lazy.LazySimpleSerDe'
        |  with serdeproperties ('field.delim'=',')
      """.stripMargin)

  hql(s"""load data local inpath "${args(0)}" into table scan_csv""")

  hql("""create table scan_rcfile (key int, value string)
        |  row format serde 'org.apache.hadoop.hive.serde2.columnar.ColumnarSerDe'
        |stored as
        |  inputformat 'org.apache.hadoop.hive.ql.io.RCFileInputFormat'
        |  outputformat 'org.apache.hadoop.hive.ql.io.RCFileOutputFormat'
      """.stripMargin)

  hql(
    """
      |from scan_csv
      |insert overwrite table scan_rcfile
      |select scan_csv.key, scan_csv.value
    """.stripMargin)
}
```

Benchmark code:

```scala
package org.apache.spark.examples.sql.hive

import org.apache.spark.sql.hive.LocalHiveContext
import org.apache.spark.{SparkConf, SparkContext}

object HiveTableScanBenchmark extends App {
  val sparkContext = new SparkContext(
    new SparkConf()
      .setMaster("local")
      .setAppName(getClass.getSimpleName.stripSuffix("$")))

  val hiveContext = new LocalHiveContext(sparkContext)

  import hiveContext._

  val scanCsv = hql("select key from scan_csv")
  val scanRcfile = hql("select key from scan_rcfile")

  val csvDuration = benchmark(scanCsv.count())
  val rcfileDuration = benchmark(scanRcfile.count())

  println(s"CSV: $csvDuration ms, RCFile: $rcfileDuration ms")

  def benchmark(f: => Unit) = {
    val begin = System.currentTimeMillis()
    f
    val end = System.currentTimeMillis()
    end - begin
  }
}
```

@marmbrus Please help review, thanks!

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #758 from liancheng/fastHiveTableScan and squashes the following commits:

4241a19 [Cheng Lian] Distinguishes sorted and possibly not sorted operations more accurately in HiveComparisonTest
cf640d8 [Cheng Lian] More HiveTableScan optimisations:
bf0e7dc [Cheng Lian] Added SortedOperation pattern to match *some* definitely sorted operations and avoid some sorting cost in HiveComparisonTest.
6d1c642 [Cheng Lian] Using ColumnProjectionUtils to optimise RCFile and ORC column pruning
eb62fd3 [Cheng Lian] [SPARK-1368] Optimized HiveTableScan
initial version of LPA

A straightforward implementation of LPA algorithm for detecting graph communities using the Pregel framework.  Amongst the growing literature on community detection algorithms in networks, LPA is perhaps the most elementary, and despite its flaws it remains a nice and simple approach.

Author: Ankur Dave <ankurdave@gmail.com>
Author: haroldsultan <haroldsultan@gmail.com>
Author: Harold Sultan <haroldsultan@gmail.com>

Closes #905 from haroldsultan/master and squashes the following commits:

327aee0 [haroldsultan] Merge pull request #2 from ankurdave/label-propagation
227a4d0 [Ankur Dave] Untabify
0ac574c [haroldsultan] Merge pull request #1 from ankurdave/label-propagation
0e24303 [Ankur Dave] Add LabelPropagationSuite
84aa061 [Ankur Dave] LabelPropagation: Fix compile errors and style; rename from LPA
9830342 [Harold Sultan] initial version of LPA
[SPARK-1820] Make GenerateMimaIgnore @DeveloperApi annotation aware.

We add all the classes annotated as `DeveloperApi` to `~/.mima-excludes`.

Author: Prashant Sharma <prashant.s@imaginea.com>
Author: nikhil7sh <nikhilsharmalnmiit@gmail.ccom>

Closes #904 from ScrapCodes/SPARK-1820/ignore-Developer-Api and squashes the following commits:

de944f9 [Prashant Sharma] Code review.
e3c5215 [Prashant Sharma] Incorporated patrick's suggestions and fixed the scalastyle build.
9983a42 [nikhil7sh] [SPARK-1820] Make GenerateMimaIgnore @DeveloperApi annotation aware
[SPARK-1566] consolidate programming guide, and general doc updates

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
[SPARK-1971] Update MIMA to compare against Spark 1.0.0

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #910 from ScrapCodes/enable-mima/spark-core and squashes the following commits:

79f3687 [Prashant Sharma] updated Mima to check against version 1.0
1e8969c [Prashant Sharma] Spark core missed out on Mima settings. So in effect we never tested spark core for mima related errors.
[SPARK-1901] worker should make sure executor has exited before updating executor's info

https://issues.apache.org/jira/browse/SPARK-1901

Author: Zhen Peng <zhenpeng01@baidu.com>

Closes #854 from zhpengg/bugfix-worker-kills-executor and squashes the following commits:

21d380b [Zhen Peng] add some error messages
506cea6 [Zhen Peng] add some docs for killProcess()
a0b9860 [Zhen Peng] [SPARK-1901] worker should make sure executor has exited before updating executor's info
Typo: and -> an

Author: Andrew Ash <andrew@andrewash.com>

Closes #927 from ash211/patch-5 and squashes the following commits:

79b577d [Andrew Ash] Typo: and -> an
updated link to mailing list

Author: nchammas <nicholas.chammas@gmail.com>

Closes #923 from nchammas/patch-1 and squashes the following commits:

65c4d18 [nchammas] updated link to mailing list
SPARK-1976: fix the misleading part in  streaming docs

Spark streaming requires at least two working threads, but the document gives the example like

import org.apache.spark.api.java.function._
import org.apache.spark.streaming._
import org.apache.spark.streaming.api._
// Create a StreamingContext with a local master
val ssc = new StreamingContext("local", "NetworkWordCount", Seconds(1))
http://spark.apache.org/docs/latest/streaming-programming-guide.html

Author: CodingCat <zhunansjtu@gmail.com>

Closes #924 from CodingCat/master and squashes the following commits:

bb89f20 [CodingCat] update streaming docs
[SPARK-1959] String "NULL" shouldn't be interpreted as null value

JIRA issue: [SPARK-1959](https://issues.apache.org/jira/browse/SPARK-1959)

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #909 from liancheng/spark-1959 and squashes the following commits:

306659c [Cheng Lian] [SPARK-1959] String "NULL" shouldn't be interpreted as null value
correct tiny comment error

Author: Chen Chao <crazyjvm@gmail.com>

Closes #928 from CrazyJvm/patch-8 and squashes the following commits:

144328b [Chen Chao] correct tiny comment error
[SPARK-1947] [SQL] Child of SumDistinct or Average should be widened to prevent overflows the same as Sum.

Child of `SumDistinct` or `Average` should be widened to prevent overflows the same as `Sum`.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #902 from ueshin/issues/SPARK-1947 and squashes the following commits:

99c3dcb [Takuya UESHIN] Insert Cast for SumDistinct and Average.
Optionally include Hive as a dependency of the REPL.

Due to the way spark-shell launches from an assembly jar, I don't think this change will affect anyone who isn't trying to launch the shell directly from sbt.  That said, it is kinda nice to be able to launch all things directly from SBT when developing.

Author: Michael Armbrust <michael@databricks.com>

Closes #801 from marmbrus/hiveRepl and squashes the following commits:

9570571 [Michael Armbrust] Optionally include Hive as a dependency of the REPL.
[SQL] SPARK-1964 Add timestamp to hive metastore type parser.

Author: Michael Armbrust <michael@databricks.com>

Closes #913 from marmbrus/timestampMetastore and squashes the following commits:

8e0154f [Michael Armbrust] Add timestamp to hive metastore type parser.
Super minor: Close inputStream in SparkSubmitArguments

`Properties#load()` doesn't close the InputStream, but it'd be closed after being GC'd anyway...

Also changed file.getName to file, because getName only shows the filename. This will show the full (possibly relative) path, which is less confusing if it's not found.

Author: Aaron Davidson <aaron@databricks.com>

Closes #914 from aarondav/tiny and squashes the following commits:

db9d072 [Aaron Davidson] Super minor: Close inputStream in SparkSubmitArguments