[SPARK-4397][Core] Change the 'since' value of '@deprecated' to '1.3.0'

As #3262 wasn't merged to branch 1.2, the `since` value of `deprecated` should be '1.3.0'.

Author: zsxwing <zsxwing@gmail.com>

Closes #3573 from zsxwing/SPARK-4397-version and squashes the following commits:

1daa03c [zsxwing] Change the 'since' value to '1.3.0'
[SPARK-4710] [mllib] Eliminate MLlib compilation warnings

Renamed StreamingKMeans to StreamingKMeansExample to avoid warning about name conflict with StreamingKMeans class.

Added import to DecisionTreeRunner to eliminate warning.

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #3568 from jkbradley/ml-compilation-warnings and squashes the following commits:

64d6bc4 [Joseph K. Bradley] Updated DecisionTreeRunner.scala and StreamingKMeans.scala to eliminate compilation warnings, including renaming StreamingKMeans to StreamingKMeansExample.
[SPARK-4708][MLLib] Make k-mean runs two/three times faster with dense/sparse sample

Note that the usage of `breezeSquaredDistance` in
`org.apache.spark.mllib.util.MLUtils.fastSquaredDistance`
is in the critical path, and `breezeSquaredDistance` is slow.
We should replace it with our own implementation.

Here is the benchmark against mnist8m dataset.

Before
DenseVector: 70.04secs
SparseVector: 59.05secs

With this PR
DenseVector: 30.58secs
SparseVector: 21.14secs

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3565 from dbtsai/kmean and squashes the following commits:

08bc068 [DB Tsai] restyle
de24662 [DB Tsai] address feedback
b185a77 [DB Tsai] cleanup
4554ddd [DB Tsai] first commit
[SPARK-4717][MLlib] Optimize BLAS library to avoid de-reference multiple times in loop

Have a local reference to `values` and `indices` array in the `Vector` object
so JVM can locate the value with one operation call. See `SPARK-4581`
for similar optimization, and the bytecode analysis.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3577 from dbtsai/blasopt and squashes the following commits:

62d38c4 [DB Tsai] formating
0316cef [DB Tsai] first commit
SPARK-2624 add datanucleus jars to the container in yarn-cluster

If `spark-submit` finds the datanucleus jars, it adds them to the driver's classpath, but does not add it to the container.

This patch modifies the yarn deployment class to copy all `datanucleus-*` jars found in `[spark-home]/libs` to the container.

Author: Jim Lim <jim@quixey.com>

Closes #3238 from jimjh/SPARK-2624 and squashes the following commits:

3633071 [Jim Lim] SPARK-2624 update documentation and comments
fe95125 [Jim Lim] SPARK-2624 keep java imports together
6c31fe0 [Jim Lim] SPARK-2624 update documentation
6690fbf [Jim Lim] SPARK-2624 add tests
d28d8e9 [Jim Lim] SPARK-2624 add spark.yarn.datanucleus.dir option
84e6cba [Jim Lim] SPARK-2624 add datanucleus jars to the container in yarn-cluster
[SPARK-4701] Typo in sbt/sbt

Modified typo.

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3560 from tsudukim/feature/SPARK-4701 and squashes the following commits:

ed2a3f1 [Masayoshi TSUZUKI] Another whitespace position error.
1af3a35 [Masayoshi TSUZUKI] [SPARK-4701] Typo in sbt/sbt
[SPARK-4715][Core] Make sure tryToAcquire won't return a negative value

ShuffleMemoryManager.tryToAcquire may return a negative value. The unit test demonstrates this bug. It will output `0 did not equal -200 granted is negative`.

Author: zsxwing <zsxwing@gmail.com>

Closes #3575 from zsxwing/SPARK-4715 and squashes the following commits:

a193ae6 [zsxwing] Make sure tryToAcquire won't return a negative value
[SPARK-4642] Add description about spark.yarn.queue to running-on-YARN document.

Added descriptions about these parameters.
- spark.yarn.queue

Modified description about the defalut value of this parameter.
- spark.yarn.submit.file.replication

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3500 from tsudukim/feature/SPARK-4642 and squashes the following commits:

ce99655 [Masayoshi TSUZUKI] better gramatically.
21cf624 [Masayoshi TSUZUKI] Removed intentionally undocumented properties.
88cac9b [Masayoshi TSUZUKI] [SPARK-4642] Documents about running-on-YARN needs update
Merge branch 'master' of github.com:apache/spark into rdd-implicit

Conflicts:
	core/src/main/scala/org/apache/spark/SparkContext.scala