[SPARK-1250] Fixed misleading comments in bin/pyspark, bin/spark-class

Fixed a couple of misleading comments in bin/pyspark and bin/spark-class. The comments make it seem like the script is looking for the Scala installation when in fact it is looking for Spark.

Author: Sumedh Mungee <smungee@gmail.com>

Closes #843 from smungee/spark-1250-fix-comments and squashes the following commits:

26870f3 [Sumedh Mungee] [SPARK-1250] Fixed misleading comments in bin/pyspark and bin/spark-class
[Docs] Correct example of creating a new SparkConf

The example code on the configuration page currently does not compile.

Author: Andrew Or <andrewor14@gmail.com>

Closes #842 from andrewor14/conf-docs and squashes the following commits:

aabff57 [Andrew Or] Correct example of creating a new SparkConf
[Minor] Move JdbcRDDSuite to the correct package

It was in the wrong package

Author: Andrew Or <andrewor14@gmail.com>

Closes #839 from andrewor14/jdbc-suite and squashes the following commits:

f948c5a [Andrew Or] cache -> cache()
b215279 [Andrew Or] Move JdbcRDDSuite to the correct package
[Typo] Stoped -> Stopped

Author: Andrew Or <andrewor14@gmail.com>

Closes #847 from andrewor14/yarn-typo and squashes the following commits:

c1906af [Andrew Or] Stoped -> Stopped
[SPARK-1519] Support minPartitions param of wholeTextFiles() in PySpark

Author: Kan Zhang <kzhang@apache.org>

Closes #697 from kanzhang/SPARK-1519 and squashes the following commits:

4f8d1ed [Kan Zhang] [SPARK-1519] Support minPartitions param of wholeTextFiles() in PySpark
[SPARK-1889] [SQL] Apply splitConjunctivePredicates to join condition while finding join ke...

...ys.

When tables are equi-joined by multiple-keys `HashJoin` should be used, but `CartesianProduct` and then `Filter` are used.
The join keys are paired by `And` expression so we need to apply `splitConjunctivePredicates` to join condition while finding join keys.

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

Closes #836 from ueshin/issues/SPARK-1889 and squashes the following commits:

fe1c387 [Takuya UESHIN] Apply splitConjunctivePredicates to join condition while finding join keys.
Configuration documentation updates

1. Add < code > to configuration options
2. List env variables in tabular format to be consistent with other pages.
3. Moved Viewing Spark Properties section up.

This is against branch-1.0, but should be cherry picked into master as well.

Author: Reynold Xin <rxin@apache.org>

Closes #851 from rxin/doc-config and squashes the following commits:

28ac0d3 [Reynold Xin] Add <code> to configuration options, and list env variables in a table.

(cherry picked from commit 75af8bd3336d09e8c691e54ae9d2358fe1bf3723)
Signed-off-by: Reynold Xin <rxin@apache.org>
[SPARK-1870] Make spark-submit --jars work in yarn-cluster mode.

Sent secondary jars to distributed cache of all containers and add the cached jars to classpath before executors start. Tested on a YARN cluster (CDH-5.0).

`spark-submit --jars` also works in standalone server and `yarn-client`. Thanks for @andrewor14 for testing!

I removed "Doesn't work for drivers in standalone mode with "cluster" deploy mode." from `spark-submit`'s help message, though we haven't tested mesos yet.

CC: @dbtsai @sryza

Author: Xiangrui Meng <meng@databricks.com>

Closes #848 from mengxr/yarn-classpath and squashes the following commits:

23e7df4 [Xiangrui Meng] rename spark.jar to __spark__.jar and app.jar to __app__.jar to avoid confliction apped $CWD/ and $CWD/* to the classpath remove unused methods
a40f6ed [Xiangrui Meng] standalone -> cluster
65e04ad [Xiangrui Meng] update spark-submit help message and add a comment for yarn-client
11e5354 [Xiangrui Meng] minor changes
3e7e1c4 [Xiangrui Meng] use sparkConf instead of hadoop conf
dc3c825 [Xiangrui Meng] add secondary jars to classpath in yarn
Fix UISuite unit test that fails under Jenkins contention

Due to perhaps zombie processes on Jenkins, it seems that at least 10
Spark ports are in use. It also doesn't matter that the port increases
when used, it could in fact go down -- the only part that matters is
that it selects a different port rather than failing to bind.
Changed test to match this.

Thanks to @andrewor14 for helping diagnose this.

Author: Aaron Davidson <aaron@databricks.com>

Closes #857 from aarondav/tiny and squashes the following commits:

c199ec8 [Aaron Davidson] Fix UISuite unit test that fails under Jenkins contention
[SPARK-1897] Respect spark.jars (and --jars) in spark-shell

Spark shell currently overwrites `spark.jars` with `ADD_JARS`. In all modes except yarn-cluster, this means the `--jar` flag passed to `bin/spark-shell` is also discarded. However, in the [docs](http://people.apache.org/~pwendell/spark-1.0.0-rc7-docs/scala-programming-guide.html#initializing-spark), we explicitly tell the users to add the jars this way.

Author: Andrew Or <andrewor14@gmail.com>

Closes #849 from andrewor14/shell-jars and squashes the following commits:

928a7e6 [Andrew Or] ',' -> "," (minor)
afc357c [Andrew Or] Handle spark.jars == "" in SparkILoop, not SparkSubmit
c6da113 [Andrew Or] Do not set spark.jars to ""
d8549f7 [Andrew Or] Respect spark.jars and --jars in spark-shell
[SPARK-1896] Respect spark.master (and --master) before MASTER in spark-shell

The hierarchy for configuring the Spark master in the shell is as follows:
```
MASTER > --master > spark.master (spark-defaults.conf)
```
This is inconsistent with the way we run normal applications, which is:
```
--master > spark.master (spark-defaults.conf) > MASTER
```

I was trying to run a shell locally on a standalone cluster launched through the ec2 scripts, which automatically set `MASTER` in spark-env.sh. It was surprising to me that `--master` didn't take effect, considering that this is the way we tell users to set their masters [here](http://people.apache.org/~pwendell/spark-1.0.0-rc7-docs/scala-programming-guide.html#initializing-spark).

Author: Andrew Or <andrewor14@gmail.com>

Closes #846 from andrewor14/shell-master and squashes the following commits:

2cb81c9 [Andrew Or] Respect spark.master before MASTER in REPL
Updated scripts for auditing releases

- Added script to automatically generate change list CHANGES.txt
- Added test for verifying linking against maven distributions of `spark-sql` and `spark-hive`
- Added SBT projects for testing functionality of `spark-sql` and `spark-hive`
- Fixed issues in existing tests that might have come up because of changes in Spark 1.0

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #844 from tdas/update-dev-scripts and squashes the following commits:

25090ba [Tathagata Das] Added missing license
e2e20b3 [Tathagata Das] Updated tests for auditing releases.
Update LBFGSSuite.scala

the same reason as https://github.com/apache/spark/pull/588

Author: baishuo(白硕) <vc_java@hotmail.com>

Closes #815 from baishuo/master and squashes the following commits:

6876c1e [baishuo(白硕)] Update LBFGSSuite.scala
[SPARK-1900 / 1918] PySpark on YARN is broken

If I run the following on a YARN cluster
```
bin/spark-submit sheep.py --master yarn-client
```
it fails because of a mismatch in paths: `spark-submit` thinks that `sheep.py` resides on HDFS, and balks when it can't find the file there. A natural workaround is to add the `file:` prefix to the file:
```
bin/spark-submit file:/path/to/sheep.py --master yarn-client
```
However, this also fails. This time it is because python does not understand URI schemes.

This PR fixes this by automatically resolving all paths passed as command line argument to `spark-submit` properly. This has the added benefit of keeping file and jar paths consistent across different cluster modes. For python, we strip the URI scheme before we actually try to run it.

Much of the code is originally written by @mengxr. Tested on YARN cluster. More tests pending.

Author: Andrew Or <andrewor14@gmail.com>

Closes #853 from andrewor14/submit-paths and squashes the following commits:

0bb097a [Andrew Or] Format path correctly before adding it to PYTHONPATH
323b45c [Andrew Or] Include --py-files on PYTHONPATH for pyspark shell
3c36587 [Andrew Or] Improve error messages (minor)
854aa6a [Andrew Or] Guard against NPE if user gives pathological paths
6638a6b [Andrew Or] Fix spark-shell jar paths after #849 went in
3bb0359 [Andrew Or] Update more comments (minor)
2a1f8a0 [Andrew Or] Update comments (minor)
6af2c77 [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-paths
a68c4d1 [Andrew Or] Handle Windows python file path correctly
427a250 [Andrew Or] Resolve paths properly for Windows
a591a4a [Andrew Or] Update tests for resolving URIs
6c8621c [Andrew Or] Move resolveURIs to Utils
db8255e [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-paths
f542dce [Andrew Or] Fix outdated tests
691c4ce [Andrew Or] Ignore special primary resource names
5342ac7 [Andrew Or] Add missing space in error message
02f77f3 [Andrew Or] Resolve command line arguments to spark-submit properly
SPARK-1911: Emphasize that Spark jars should be built with Java 6.

This commit requires the user to manually say "yes" when buiding Spark
without Java 6. The prompt can be bypassed with a flag (e.g. if the user
is scripting around make-distribution).

Author: Patrick Wendell <pwendell@gmail.com>

Closes #859 from pwendell/java6 and squashes the following commits:

4921133 [Patrick Wendell] Adding Pyspark Notice
fee8c9e [Patrick Wendell] SPARK-1911: Emphasize that Spark jars should be built with Java 6.
[SPARK-1886] check executor id existence when executor exit

Author: Zhen Peng <zhenpeng01@baidu.com>

Closes #827 from zhpengg/bugfix-executor-id-not-found and squashes the following commits:

cd8bb65 [Zhen Peng] bugfix: check executor id existence when executor exit
[SPARK-1913][SQL] Bug fix: column pruning error in Parquet support

JIRA issue: [SPARK-1913](https://issues.apache.org/jira/browse/SPARK-1913)

When scanning Parquet tables, attributes referenced only in predicates that are pushed down are not passed to the `ParquetTableScan` operator and causes exception.

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

Closes #863 from liancheng/spark-1913 and squashes the following commits:

f976b73 [Cheng Lian] Addessed the readability issue commented by @rxin
f5b257d [Cheng Lian] Added back comments deleted by mistake
ae60ab3 [Cheng Lian] [SPARK-1913] Attributes referenced only in predicates pushed down should remain in ParquetTableScan operator
spark-submit: add exec at the end of the script

Add an 'exec' at the end of the spark-submit script, to avoid keeping a
bash process hanging around while it runs.  This makes ps look a little
bit nicer.

Author: Colin Patrick Mccabe <cmccabe@cloudera.com>

Closes #858 from cmccabe/SPARK-1907 and squashes the following commits:

7023b64 [Colin Patrick Mccabe] spark-submit: add exec at the end of the script
[SPARK-1822] SchemaRDD.count() should use query optimizer

Author: Kan Zhang <kzhang@apache.org>

Closes #841 from kanzhang/SPARK-1822 and squashes the following commits:

2f8072a [Kan Zhang] [SPARK-1822] Minor style update
cf4baa4 [Kan Zhang] [SPARK-1822] Adding Scaladoc
e67c910 [Kan Zhang] [SPARK-1822] SchemaRDD.count() should use optimizer
Added PEP8 style configuration file.

This sets the max line length to 100 as a PEP8 exception.

Author: Reynold Xin <rxin@apache.org>

Closes #872 from rxin/pep8 and squashes the following commits:

2f26029 [Reynold Xin] Added PEP8 style configuration file.