[ENGINE] Fix updates dynamic settings in InternalEngineHolder

After the refactoring in #8784 some settings didn't get passed to the
actual engine and there exists a race if the settings are updated while
the engine is started such that the actual starting engine doesn't see
the latest settings. This commit fixes the concurrency issue as well as
adds tests to ensure the settings are reflected.
[GEO] Fix for NPE enclosed in SearchParseException for a "geo_shape" filter or query

This fix adds better error handling for parsing multipoint, linestring, and polygon GeoJSONs.  Current logic throws a NPE when parsing a multipoint, linestring, or polygon that does not comply with the GeoJSON specification. That is, if a user provides a single coordinate instead of an array of coordinates, or array of linestrings, the ShapeParser throws a NPE wrapped in a SearchParseException instead of a more useful error message.

Closes #8432
[core] add best_compression option for Lucene 5.0

Upgrades lucene to latest, and supports the BEST_COMPRESSION parameter
now supported (with backwards compatibility, etc) in Lucene.
This option uses deflate, tuned for highly compressible data.

index.codec::
The default value compresses stored data with LZ4 compression, but
this can be set to best_compression for a higher compression ratio,
at the expense of slower stored fields performance.

IMO its safest to implement as a named codec here, because ES already
has logic to handle this correctly, and because its unrealistic to have
a plethora of options to Lucene's default codec... we are practically
limited in Lucene to what we can support with back compat, so I don't
think we should overengineer this and add additional unnecessary plumbing.

See also:
https://issues.apache.org/jira/browse/LUCENE-5914
https://issues.apache.org/jira/browse/LUCENE-6089
https://issues.apache.org/jira/browse/LUCENE-6090
https://issues.apache.org/jira/browse/LUCENE-6100

Closes #8863
Test: create private store for these test cases
Mappings: Fix Get field mapping api with pretty flag

Closes #6552
[ENGINE] Remove engine related command classes

Todaqy we pass structs to the engine to call optimize / refresh and flush.
This commit cleans up this logic to reduce complexity in the engine.
[SCRIPT] ScriptService can deadlock entire nodes if script index is recovering

we currently have operationThreaded set to false when indexing a script. This setting
means that if we are executing the operation locally that we don't spawn a new thread for
it althought incoming thread in this case is the network thread. Now sicne we are indexing here
the engine is currently recovering which sometimes locks the engine for finalization blocks on
a network call waiting for the recovery target to come back the internal lock in engine will never be
released since we are waiting with our network thread for it to be released.
HTTP: Add 'http.publish_port' setting to the HTTP module

This change adds a 'http.publish_port' setting to the HTTP module to configure
the port which HTTP clients should use when communicating with the node. This
is useful when running on a bridged network interface or when running behind
a proxy or firewall.

Closes #8807
Closes #8137
Packaging: Add java7/8 java-package paths to debian init script

If you use the java-package tool to create java packages, those
paths also should be added to the debian init script.

Also updated the docs, that it is ok to install java8.

Closes #7383
[GATEWAY] Cleanup LocalGatewayShardsState

This commit tries to cleanup LocalGatewayShardsState to be more efficient
and easier to understand.
added unittest