SPARK-1387. Update build plugins, avoid plugin version warning, centralize versions

Another handful of small build changes to organize and standardize a bit, and avoid warnings:

- Update Maven plugin versions for good measure
- Since plugins need maven 3.0.4 already, require it explicitly (<3.0.4 had some bugs anyway)
- Use variables to define versions across dependencies where they should move in lock step
- ... and make this consistent between Maven/SBT

OK, I also updated the JIRA URL while I was at it here.

Author: Sean Owen <sowen@cloudera.com>

Closes #291 from srowen/SPARK-1387 and squashes the following commits:

461eca1 [Sean Owen] Couldn't resist also updating JIRA location to new one
c2d5cc5 [Sean Owen] Update plugins and Maven version; use variables consistently across Maven/SBT to define dependency versions that should stay in step.
SPARK-1349: spark-shell gets its own command history

Currently, spark-shell shares its command history with scala repl.

This fix is simply a modification of the default FileBackedHistory file setting:
https://github.com/scala/scala/blob/master/src/repl/scala/tools/nsc/interpreter/session/FileBackedHistory.scala#L77

Author: Aaron Davidson <aaron@databricks.com>

Closes #267 from aarondav/repl and squashes the following commits:

f9c62d2 [Aaron Davidson] SPARK-1349: spark-shell gets its own command history separate from scala repl
SPARK-1314: Use SPARK_HIVE to determine if we include Hive in packaging

Previously, we based our decision regarding including datanucleus jars based on the existence of a spark-hive-assembly jar, which was incidentally built whenever "sbt assembly" is run. This means that a typical and previously supported pathway would start using hive jars.

This patch has the following features/bug fixes:

- Use of SPARK_HIVE (default false) to determine if we should include Hive in the assembly jar.
- Analagous feature in Maven with -Phive (previously, there was no support for adding Hive to any of our jars produced by Maven)
- assemble-deps fixed since we no longer use a different ASSEMBLY_DIR
- avoid adding log message in compute-classpath.sh to the classpath :)

Still TODO before mergeable:
- We need to download the datanucleus jars outside of sbt. Perhaps we can have spark-class download them if SPARK_HIVE is set similar to how sbt downloads itself.
- Spark SQL documentation updates.

Author: Aaron Davidson <aaron@databricks.com>

Closes #237 from aarondav/master and squashes the following commits:

5dc4329 [Aaron Davidson] Typo fixes
dd4f298 [Aaron Davidson] Doc update
dd1a365 [Aaron Davidson] Eliminate need for SPARK_HIVE at runtime by d/ling datanucleus from Maven
a9269b5 [Aaron Davidson] [WIP] Use SPARK_HIVE to determine if we include Hive in packaging
SPARK-1154: Clean up app folders in worker nodes

This is a fix for [SPARK-1154](https://issues.apache.org/jira/browse/SPARK-1154).   The issue is that worker nodes fill up with a huge number of app-* folders after some time.  This change adds a periodic cleanup task which asynchronously deletes app directories older than a configurable TTL.

Two new configuration parameters have been introduced:
  spark.worker.cleanup_interval
  spark.worker.app_data_ttl

This change does not include moving the downloads of application jars to a location outside of the work directory.  We will address that if we have time, but that potentially involves caching so it will come either as part of this PR or a separate PR.

Author: Evan Chan <ev@ooyala.com>
Author: Kelvin Chu <kelvinkwchu@yahoo.com>

Closes #288 from velvia/SPARK-1154-cleanup-app-folders and squashes the following commits:

0689995 [Evan Chan] CR from @aarondav - move config, clarify for standalone mode
9f10d96 [Evan Chan] CR from @pwendell - rename configs and add cleanup.enabled
f2f6027 [Evan Chan] CR from @andrewor14
553d8c2 [Kelvin Chu] change the variable name to currentTimeMillis since it actually tracks in seconds
8dc9cb5 [Kelvin Chu] Fixed a bug in Utils.findOldFiles() after merge.
cb52f2b [Kelvin Chu] Change the name of findOldestFiles() to findOldFiles()
72f7d2d [Kelvin Chu] Fix a bug of Utils.findOldestFiles(). file.lastModified is returned in milliseconds.
ad99955 [Kelvin Chu] Add unit test for Utils.findOldestFiles()
dc1a311 [Evan Chan] Don't recompute current time with every new file
e3c408e [Evan Chan] Document the two new settings
b92752b [Evan Chan] SPARK-1154: Add a periodic task to clean up app directories
SPARK-1431: Allow merging conflicting pull requests

Sometimes if there is a small conflict it's nice to be able to just
manually fix it up rather than have another RTT with the contributor.

Author: Patrick Wendell <pwendell@gmail.com>

Closes #342 from pwendell/merge-conflicts and squashes the following commits:

cdce61a [Patrick Wendell] SPARK-1431: Allow merging conflicting pull requests
Merge branch 'master' into eval