[SPARK-4379][Core] Change Exception to SparkException in checkpoint

It's better to change to SparkException. However, it's a breaking change since it will change the exception type.

Author: zsxwing <zsxwing@gmail.com>

Closes #3241 from zsxwing/SPARK-4379 and squashes the following commits:

409f3af [zsxwing] Change Exception to SparkException in checkpoint
[SPARK-4363][Doc] Update the Broadcast example

Author: zsxwing <zsxwing@gmail.com>

Closes #3226 from zsxwing/SPARK-4363 and squashes the following commits:

8109914 [zsxwing] Update the Broadcast example
[SPARK-4260] Httpbroadcast should set connection timeout.

Httpbroadcast sets read timeout but doesn't set connection timeout.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #3122 from sarutak/httpbroadcast-timeout and squashes the following commits:

c7f3a56 [Kousuke Saruta] Added Connection timeout for Http Connection to HttpBroadcast.scala
Added contains(key) to Metadata

Add contains(key) to org.apache.spark.sql.catalyst.util.Metadata to test the existence of a key. Otherwise, Class Metadata's get methods may throw NoSuchElement exception if the key does not exist.
Testcases are added to MetadataSuite as well.

Author: kai <kaizeng@eecs.berkeley.edu>

Closes #3273 from kai-zeng/metadata-fix and squashes the following commits:

74b3d03 [kai] Added contains(key) to Metadata
[SPARK-2321] Several progress API improvements / refactorings

This PR refactors / extends the status API introduced in #2696.

- Change StatusAPI from a mixin trait to a class.  Before, the new status API methods were directly accessible through SparkContext, whereas now they're accessed through a `sc.statusAPI` field.  As long as we were going to add these methods directly to SparkContext, the mixin trait seemed like a good idea, but this might be simpler to reason about and may avoid pitfalls that I've run into while attempting to refactor other parts of SparkContext to use mixins (see #3071, for example).
- Change the name from SparkStatusAPI to SparkStatusTracker.
- Make `getJobIdsForGroup(null)` return ids for jobs that aren't associated with any job group.
- Add `getActiveStageIds()` and `getActiveJobIds()` methods that return the ids of whatever's currently active in this SparkContext.  This should simplify davies's progress bar code.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3197 from JoshRosen/progress-api-improvements and squashes the following commits:

30b0afa [Josh Rosen] Rename SparkStatusAPI to SparkStatusTracker.
d1b08d8 [Josh Rosen] Add missing newlines
2cc7353 [Josh Rosen] Add missing file.
d5eab1f [Josh Rosen] Add getActive[Stage|Job]Ids() methods.
a227984 [Josh Rosen] getJobIdsForGroup(null) should return jobs for default group
c47e294 [Josh Rosen] Remove StatusAPI mixin trait.
[SPARK-4419] Upgrade snappy-java to 1.1.1.6

This upgrades snappy-java to 1.1.1.6, which includes a patch that improves error messages when attempting to deserialize empty inputs using SnappyInputStream (see xerial/snappy-java#89).

We previously tried up upgrade to 1.1.1.5 in #2911 but reverted that patch after discovering a memory leak in snappy-java.  This should leak have been fixed in 1.1.1.6, though (see xerial/snappy-java#92).

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3287 from JoshRosen/SPARK-4419 and squashes the following commits:

5d6f4cc [Josh Rosen] [SPARK-4419] Upgrade snappy-java to 1.1.1.6.
[SPARK-4426][SQL][Minor] The symbol of BitwiseOr is wrong, should not be '&'

The symbol of BitwiseOr is defined as '&' but I think it's wrong. It should be '|'.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #3284 from sarutak/bitwise-or-symbol-fix and squashes the following commits:

aff4be5 [Kousuke Saruta] Fixed symbol of BitwiseOr
[SPARK-4393] Fix memory leak in ConnectionManager ACK timeout TimerTasks; use HashedWheelTimer

This patch is intended to fix a subtle memory leak in ConnectionManager's ACK timeout TimerTasks: in the old code, each TimerTask held a reference to the message being sent and a cancelled TimerTask won't necessarily be garbage-collected until it's scheduled to run, so this caused huge buildups of messages that weren't garbage collected until their timeouts expired, leading to OOMs.

This patch addresses this problem by capturing only the message ID in the TimerTask instead of the whole message, and by keeping a WeakReference to the promise in the TimerTask.  I've also modified this code to use Netty's HashedWheelTimer, whose performance characteristics should be better for this use-case.

Thanks to cristianopris for narrowing down this issue!

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3259 from JoshRosen/connection-manager-timeout-bugfix and squashes the following commits:

afcc8d6 [Josh Rosen] Address rxin's review feedback.
2a2e92d [Josh Rosen] Keep only WeakReference to promise in TimerTask;
0f0913b [Josh Rosen] Spelling fix: timout => timeout
3200c33 [Josh Rosen] Use Netty HashedWheelTimer
f847dd4 [Josh Rosen] Don't capture entire message in ACK timeout task.
[SPARK-4309][SPARK-4407][SQL] Date type support for Thrift server, and fixes for complex types

SPARK-4407 was detected while working on SPARK-4309. Merged these two into a single PR since 1.2.0 RC is approaching.

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Author: Cheng Lian <lian@databricks.com>

Closes #3178 from liancheng/date-for-thriftserver and squashes the following commits:

6f71d0b [Cheng Lian] Makes toHiveString static
26fa955 [Cheng Lian] Fixes complex type support in Hive 0.13.1 shim
a92882a [Cheng Lian] Updates HiveShim for 0.13.1
73f442b [Cheng Lian] Adds Date support for HiveThriftServer2 (Hive 0.12.0)
Revert "[SPARK-4309][SPARK-4407][SQL] Date type support for Thrift server, and fixes for complex types"

Author: Michael Armbrust <michael@databricks.com>

Closes #3292 from marmbrus/revert4309 and squashes the following commits:

808e96e [Michael Armbrust] Revert "[SPARK-4309][SPARK-4407][SQL] Date type support for Thrift server, and fixes for complex types"
[SPARK-4422][MLLIB]In some cases, Vectors.fromBreeze get wrong results.

cc mengxr

Author: GuoQiang Li <witgo@qq.com>

Closes #3281 from witgo/SPARK-4422 and squashes the following commits:

5f1fa5e [GuoQiang Li] import order
50783bd [GuoQiang Li] review commits
7a10123 [GuoQiang Li] In some cases, Vectors.fromBreeze get wrong results.
[SPARK-4410][SQL] Add support for external sort

Adds a new operator that uses Spark's `ExternalSort` class.  It is off by default now, but we might consider making it the default if benchmarks show that it does not regress performance.

Author: Michael Armbrust <michael@databricks.com>

Closes #3268 from marmbrus/externalSort and squashes the following commits:

48b9726 [Michael Armbrust] comments
b98799d [Michael Armbrust] Add test
afd7562 [Michael Armbrust] Add support for external sort.
Update old version to 1.2, add temporary 1.2 repo.
Bumping version to 1.3.0-SNAPSHOT.
Merge branch 'master' into version-1.3
Add another exclusion.