Tests: Add more assertions to ExistsMissingTests.
Internal: Don't let `took` be negative.

`took` is computed based on the system clock and can be negative if the clock
time was updated during the execution of the search request. This commit
protects against these cases by replacing `took` with 1 if the elapsed time is
negative.

Close #7968
Admin: show open and closed indices in _cat/indices

When asking for `GET /_cat/indices?v`, you can now retrieve closed indices in addition to opened ones.

```
health status index              pri rep docs.count docs.deleted store.size pri.store.size
yellow open   .marvel-2014.05.21   1   1       8792            0     21.7mb         21.7mb
       close  test
yellow open   .marvel-2014.05.22   1   1       3871            0     10.7mb         10.7mb
red    open   .marvel-2014.05.27   1   1
```

Closes #7907.
Closes #7936.
Aggs fix - background count for docs should include deleted docs otherwise a term’s docFreq (which includes deleted docs) can exceed the number of docs reported in the index and cause an exception.
The randomisation that deletes documents is also removed from tests as this doc-accounting change would mean the specific scores being expected in tests would now be subject to random variability and so fail.

Closes #7951
Tests: Improve BWC preconditions to error cleanly when wire formats differ.

closes #7966
Term Vectors/MLT Query: support for different analyzers than default at field

This adds a `per_field_analyzer` parameter to the Term Vectors API, which
allows to override the default analyzer at the field. If the field already
stores term vectors, then they will be re-generated. Since the MLT Query uses
the Term Vectors API under its hood, this commits also adds the same ability
to the MLT Query, thereby allowing users to fine grain how each field item
should be processed and analyzed.

Closes #7801
Fix NPE in ScriptService when script file with no extension is deleted

Fixes #7689
Snapshot/Restore: Make sure indices cannot be renamed into restored aliases

Fixes #7915
Aggregations: makes script params consistent with other APIs in scripted_metric

This change removes the script_type parameter form the Scripted Metric Aggregation and adds support for _file and _id suffixes to the init_script, map_script, combine_script and reduce_script parameters to make defining the source of the script consistent with the other APIs which use the ScriptService
Search: add `format` support for date range filter and queries

When the date format is defined in mapping, you can not use another format when querying using range date query or filter.

For example, this won't work:

```
DELETE /test

PUT /test/t/1
{
  "date": "2014-01-01"
}

GET /test/_search
{
  "query": {
    "filtered": {
      "filter": {
        "range": {
          "date": {
            "from": "01/01/2014"
          }
        }
      }
    }
  }
}
```

It causes:

```
Caused by: org.elasticsearch.ElasticsearchParseException: failed to parse date field [01/01/2014], tried both date format [dateOptionalTime], and timestamp number
```

It could be nice if we can support at query time another date format just like we support `analyzer` at search time on String fields.

Something like:

```
GET /test/_search
{
  "query": {
    "filtered": {
      "filter": {
        "range": {
          "date": {
            "from": "01/01/2014",
            "format": "dd/MM/yyyy"
          }
        }
      }
    }
  }
}
```

Same for queries:

```
GET /test/_search
{
  "query": {
    "range": {
      "date": {
        "from": "01/01/2014",
        "format": "dd/MM/yyyy"
      }
    }
  }
}
```

Closes #7189.
Discovery: remove MasterFaultDetection.Listener.notListedOnMaster

It is never used in practice. We treat it as a master failure (using NodeDoesNotExistOnMasterException).

Closes #7995
Core: Perform write consistency just before writing on the primary shard

Before this change the write consistency change was performed on the node that receives the write request and the node that holds the primary shard. This change removes the check on the node that receives the request, since it is redundant.

Also this change moves the write consistency check on the node that holds the primary shard to a later moment after forking of the thread to perform the actual write on the primary shard.

Closes #7873
Snapshot/Restore: make it possible to delete snapshots with missing metadata file

Fixes #7980
[TEST] Fix config directory for external nodes in bwc tests

The logging configuration was expected in the path.home folder which is set to
target/JX
when running the bwc tests from the console.
Therefore the logger could not be initialized with error message:

[INFO] Failed to configure logging...
org.elasticsearch.ElasticsearchException: Failed to load logging configuration
        at org.elasticsearch.common.logging.log4j.LogConfigurator.resolveConfig(LogConfigurator.java:117)
        at org.elasticsearch.common.logging.log4j.LogConfigurator.configure(LogConfigurator.java:81)
        at org.elasticsearch.bootstrap.Bootstrap.setupLogging(Bootstrap.java:96)
        at org.elasticsearch.bootstrap.Bootstrap.main(Bootstrap.java:180)
        at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:32)
Caused by: java.nio.file.NoSuchFileException: /home/britta/es/target/J0/config
        at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
        at sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes(UnixFileAttributeViews.java:55)
        at sun.nio.fs.UnixFileSystemProvider.readAttributes(UnixFileSystemProvider.java:144)
        at sun.nio.fs.LinuxFileSystemProvider.readAttributes(LinuxFileSystemProvider.java:97)
        at java.nio.file.Files.readAttributes(Files.java:1686)
        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:109)
        at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:69)
        at java.nio.file.Files.walkFileTree(Files.java:2602)
        at org.elasticsearch.common.logging.log4j.LogConfigurator.resolveConfig(LogConfigurator.java:107)
        ... 4 more
log4j:WARN No appenders could be found for logger (node).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Setting the config directory fixes this.

Logs from external nodes are still not printed properly. They are inserted to the log
whenever the stdout is printed ([WARNING] JVM J0: stdout was not empty...)

closes #7964
[TEST] fix CurrentTestFailedMarker to reset its state after each test

The currently used method `testRunStarted` is only called before any tests have been run, we need to reset that state before each test, that's why we need to use `testStarted`.
plugins: disable support for config dir

When removing and installing again the plugin all configuration files will be removed in `config/pluginname` dir.
This is bad as users may have set and added specific configuration files.

During an install, if we detect already existing files in `config/pluginname` directory, we simply copy the new file to the same dir but we append a `.new` at the end.

Related to  #5064.

(cherry picked from commit 5da028f)
(cherry picked from commit 4cb1f95)
[SNAPSHOT] Add repository validation

Fixes #7096
Add Upgrade API

This commit does the following:
* Add the new API at the rest layer, being backed by the optimize API
  with upgrade flag, and segments api to find upgrade status.
* Add `upgrade` flag to optimize API, and deprecate `force` flag (will
  remove in master)
* Add test for both synchronous and async upgrade

closes #7884
closes #7922
Remove deprecations from master (follow up to #7922)
Fix missed places referencing optimize force flag from removal in commit 1ae8195.