This reverts commit 81cf2296.

We had an incorrent implementation of Murmur hash in Flink 1.0. This
was fixed in 641a0d43 for Flink 1.1. Then we thought that we need to
revert this in order to ensure backwards compatability between Flink
1.0 and 1.1 savepoints (81cf22). Turns out, savepoint backwards
compatability is broken for other reasons, too. Therefore, we revert
81cf22 here, ending up with a correct implementation of Murmur hash
again.

This closes #2311

Some source files had the -x flag set:

Before this change:
```
$ find . -perm +111 -type f | grep "\.java"
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/places/Attributes.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/places/BoundingBox.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/places/Places.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/Contributors.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/Coordinates.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/CurrentUserRetweet.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/Entities.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/HashTags.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/Media.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/Size.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/Symbol.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/URL.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/entities/UserMention.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/tweet/Tweet.java
./flink-contrib/flink-tweet-inputformat/src/main/java/org/apache/flink/contrib/tweetinputformat/model/User/Users.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/Graph.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/gsa/ApplyFunction.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/gsa/GatherFunction.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/gsa/GatherSumApplyIteration.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/gsa/Neighbor.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/gsa/SumFunction.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/library/GSAConnectedComponents.java
./flink-libraries/flink-gelly/src/main/java/org/apache/flink/graph/library/GSASingleSourceShortestPaths.java
./flink-libraries/flink-gelly-examples/src/main/java/org/apache/flink/graph/examples/GSASingleSourceShortestPaths.java
./flink-libraries/flink-gelly-examples/src/test/java/org/apache/flink/graph/test/GatherSumApplyITCase.java
./flink-runtime/src/main/java/org/apache/flink/runtime/executiongraph/ExecutionGraph.java
```

After this change:
```
$ find . -perm +111 -type f | grep "\.java"
```

This closes #2310

This closes #2308

The json module is bundled with Ruby from 1.9.0 and upwards. This
cures dependency problems with different versions of Ruby.

This closes #2307.

Closes #2299

This closes #2232.

- fail if config couldn't be loaded
- remove duplicate api methods
- remove undocumented XML loading feature
- generate yaml conf in tests instead of xml conf
- only load one config file instead of all xml or yaml files (flink-conf.yaml)
- make globalconfiguration non-global and remove static SINGLETON
- fix test cases
- add test cases

This closes #2123

This also updates documentation and tests.

Reporters can now be specified like this:

metrics.reporters: foo,bar

metrics.reporter.foo.class: JMXReporter.class
metrics.reporter.foo.port: 10

metrics.reporter.bar.class: GangliaReporter.class
metrics.reporter.bar.port: 11
metrics.reporter.bar.something: 42

Unfortunately, we can't deploy snapshots atomically using the Nexus
repository. The staged process which leads to an atomic deployment is
only designed to work for releases. Best we can do is to retry
deploying artifacts in case of failures.

- introduce retry in case of failure of snapshot deployment
- simplify deployment script

This closes #2296

- Add YarnFlinkResourceManager test to reaccept task manager registrations from a re-elected job manager

- Remove unnecessary sync logic between JobManager and ResourceManager

- Avoid duplicate reigstration attempts in case of a refused registration

- Add test case to check that not an excessive amount of RegisterTaskManager messages are sent

- Remove containersLaunched from YarnFlinkResourceManager and instead not clearing registeredWorkers when JobManager loses leadership

- Let YarnFlinkResourceManagerTest extend TestLogger

- Harden YarnFlinkResourceManager.getContainersFromPreviousAttempts

- Add FatalErrorOccurred message handler to FlinkResourceManager;
  Increase timeout for YarnFlinkResourceManagerTest;
  Add additional constructor to TestingYarnFlinkResourceManager for tests

- Rename registeredWorkers field into startedWorkers
Additionally, the RegisterResource message is renamed into NotifyResourceStarted which
tells the RM that a resource has been started. This reflects the current semantics of
the startedWorkers map in the resource manager.

- Fix concurrency issues in TestingLeaderRetrievalService

This closes #2257

- moved user-facing API to 'flink-metrics/flink-metrics-core'
- moved JMXReporter to 'flink-metrics/flink-metrics-jmx'
- moved remaining metric classes to 'flink-runtime'

This closes #2226

This closes #2286

This closes #2278.

Savepoints were previously persisted without any meta data using default
Java serialization of `CompletedCheckpoint`. This commit introduces a
savepoint interface with version-specific serializers and stores
savepoints with meta data.

Savepoints expose a version number and a Collection<TaskState> for
savepoint restore.

Currently, there is only one savepoint version:

SavepointV0 (Flink 1.1): This is the current savepoint version, which
holds a reference to the Checkpoint task state collection, but is
serialized with a custom serializater not relying on default Java
serialization. Therefore, it should not happen again that we need to
stick to certain classes in future Flink versions.

The savepoints are stored in `FsSavepointStore` with the following
format:

MagicNumber SavepointVersion Savepoint
  - MagicNumber => int
  - SavepointVersion => int (returned by Savepoint#getVersion())
  - Savepoint => bytes (serialized via version-specific SavepointSerializer)

The header is minimal (magic number, version). All savepoint-specific
meta data can be moved to the savepoint itself. This is also were we
would have to add new meta data in future versions, allowing us to
differentiate between different savepoint versions when we change the
serialization stack.

All savepoint related classes have been moved from checkpoint to a new
sub package `checkpoint.savepoint`.

This closes #2194.

This closes #2162.

The default maximum akka transfer size is 10 MB. This commit reduces the
number of generator blocks from 2^20 to 2^15 which removes the limit on
graph size. The original limit of one millions blocks was intended to
future-proof scalability.

This is a temporary fix as graph generation will be reworked in FLINK-3997.

This closes #2233

This closes #2280.

This closes #2292.

This closes #2283.

The `BlobServer` acts as a local cache for uploaded BLOBs. The life-cycle of
each BLOB is bound to the life-cycle of the `BlobServer`. If the BlobServer
shuts down (on JobManager shut down), all local files will be removed.

With HA, BLOBs are persisted to another file system (e.g. HDFS) via the
`BlobStore` in order to have BLOBs available after a JobManager failure (or
shut down). These BLOBs are only allowed to be removed when the job that
requires them enters a globally terminal state (`FINISHED`, `CANCELLED`,
`FAILED`).

This commit removes the `BlobStore` clean up call from the `BlobServer`
shutdown. The `BlobStore` files will only be cleaned up via the
`BlobLibraryCacheManager`'s' clean up task (periodically or on
BlobLibraryCacheManager shutdown). This means that there is a chance that
BLOBs will linger around after the job has terminated, if the job manager
fails before the clean up.

This closes #2256.

Prevents the CheckpointCommitter from failing a job, if either
commitCheckpoint() or isCheckpointCommitter() failed. Instead, we will
try again on the next notify().

This closes #2287

The user must now specify the ID type as "integer" or "string" when
reading a graph from a CSV file.

This closes #2250

This closes #2248

Suspended jobs were leading to shutdown of the checkpoint coordinator
and hence removal of checkpoint state. For standalone recovery mode
this is OK as no state can be recovered anyways (unchanged in this PR).
For HA though this lead to removal of checkpoint state, which we
actually want to keep for recovery.

We have the following behaviour now:

-----------+------------+-------------------
           | Standalone | High Availability
-----------+------------+-------------------
 SUSPENDED |  Discard   |       Keep
-----------+------------+-------------------
 FINISHED/ |  Discard   |     Discard
 FAILED/   |            |
 CANCELED  |            |
-----------+------------+-------------------

This closes #2276.

This closes #2284.

This closes #2279

This PR adds a JM metric which shows the time it took to restart a job. The time is
measured between entering the JobStatus.RESTARTING and reaching the JobStatus.RUNNING
state. During this time, the restarting time is continuously updated. The metric only
shows the time for the last restart attempt. The metric is published in the job metric
group under the name of "restartingTime".

This closes #2271.