Update command flags

Fixes #5422

docs/static/include/pluginbody.asciidoc

@@ -883,7 +883,7 @@ time.
 
 **Version messaging from Logstash**
 
-If you start Logstash with the `--verbose` flag, you will see messages like
+If you start Logstash with the `--log.level verbose` flag, you will see messages like
 these to indicate the relative maturity indicated by the plugin version number:
 
 ** **0.1.x**

docs/static/life-of-an-event.asciidoc

@@ -83,7 +83,7 @@ For more information about the available codecs, see
 
 Logstash keeps all events in main memory during processing. Logstash responds to a SIGTERM by attempting to halt inputs and waiting for pending events to finish processing before shutting down. When the pipeline cannot be flushed due to a stuck output or filter, Logstash waits indefinitely. For example, when a pipeline sends output to a database that is unreachable by the Logstash instance, the instance waits indefinitely after receiving a SIGTERM.
 
-To enable Logstash to detect these situations and terminate with a stalled pipeline, use the `--allow-unsafe-shutdown` flag.
+To enable Logstash to detect these situations and terminate with a stalled pipeline, use the `--pipeline.unsafe_shutdown` flag.
 
 WARNING: Unsafe shutdowns, force-kills of the Logstash process, or crashes of the Logstash process for any other reason result in data loss. Shut down Logstash safely whenever possible.
 

docs/static/plugin-manager.asciidoc

@@ -57,14 +57,14 @@ bin/logstash-plugin install /path/to/logstash-output-kafka-1.0.0.gem
 
 [[installing-local-plugins-path]]
 [float]
-==== Advanced: Using `--pluginpath`
+==== Advanced: Using `--path.plugins`
 
-Using the `--pluginpath` flag, you can load a plugin source code located on your file system. Typically this is used by
+Using the Logstash `--path.plugins` flag, you can load a plugin source code located on your file system. Typically this is used by
 developers who are iterating on a custom plugin and want to test it before creating a ruby gem.
 
 [source,shell]
 ----------------------------------
-bin/logstash --pluginpath /opt/shared/lib/logstash/input/my-custom-plugin-code.rb
+bin/logstash --path.plugins /opt/shared/lib/logstash/input/my-custom-plugin-code.rb
 ----------------------------------
 
 [[updating-plugins]]

docs/static/reloading-config.asciidoc

@@ -4,19 +4,19 @@
 Starting with Logstash 2.3, you can set Logstash to detect and reload configuration
 changes automatically.
 
-To enable automatic config reloading, start Logstash with the `--auto-reload` (or `-r`)
+To enable automatic config reloading, start Logstash with the `--config.reload.automatic` (or `-r`)
 command-line option specified. For example:
 
 [source,shell]
 ----------------------------------
-bin/logstash –f apache.config --auto-reload
+bin/logstash –f apache.config --config.reload.automatic
 ----------------------------------
 
-NOTE: The `--auto-reload` option is not available when you specify the `-e` flag to pass
+NOTE: The `--config.reload.automatic` option is not available when you specify the `-e` flag to pass
 in  configuration settings from the command-line.
 
 By default, Logstash checks for configuration changes every 3 seconds. To change this interval,
-use the `--reload-interval <seconds>` option,  where `seconds` specifies how often Logstash
+use the `----config.reload.interval <seconds>` option,  where `seconds` specifies how often Logstash
 checks the config files for changes. 
 
 If Logstash is already running without auto-reload enabled, you can force Logstash to

docs/static/stalled-shutdown.asciidoc

@@ -20,19 +20,19 @@ Logstash has a stall detection mechanism that analyzes the behavior of the pipel
 This mechanism produces periodic information about the count of inflight events in internal queues and a list of busy
 worker threads.
 
-To enable Logstash to forcibly terminate in the case of a stalled shutdown, use the `--allow-unsafe-shutdown` flag when
+To enable Logstash to forcibly terminate in the case of a stalled shutdown, use the `--pipeline.unsafe_shutdown` flag when
 you start Logstash.
 
 [[shutdown-stall-example]]
 ==== Stall Detection Example
 
 In this example, slow filter execution prevents the pipeline from clean shutdown. By starting Logstash with the
-`--allow-unsafe-shutdown` flag, quitting with *Ctrl+C* results in an eventual shutdown that loses 20 events.
+`--pipeline.unsafe_shutdown` flag, quitting with *Ctrl+C* results in an eventual shutdown that loses 20 events.
 
 ========
 [source,shell]
 % bin/logstash -e 'input { generator { } } filter { ruby { code => "sleep 10000" } } \
-                     output { stdout { codec => dots } }' -w 1 --allow-unsafe-shutdown
+                     output { stdout { codec => dots } }' -w 1 --pipeline.unsafe_shutdown
 Default settings used: Filter workers: 1
 Logstash startup completed
 ^CSIGINT received. Shutting down the pipeline. {:level=>:warn}
@@ -60,4 +60,4 @@ The shutdown process appears to be stalled due to busy or blocked plugins. Check
 Forcefully quitting logstash.. {:level=>:fatal}
 ========
 
-When `--allow-unsafe-shutdown` isn't enabled, Logstash continues to run and produce these reports periodically.
+When `--pipeline.unsafe_shutdown` isn't enabled, Logstash continues to run and produce these reports periodically.

docs/static/upgrading.asciidoc

@@ -17,7 +17,7 @@ This procedure uses <<package-repositories,package managers>> to upgrade Logstas
 2. Using the directions in the _Package Repositories_ section, update your repository links to point to the 2.0 repositories
 instead of the previous version.
 3. Run the `apt-get upgrade logstash` or `yum update logstash` command as appropriate for your operating system.
-4. Test your configuration file with the `logstash --configtest -f <configuration-file>` command. Configuration options for
+4. Test your configuration file with the `logstash --config.test_and_exit -f <configuration-file>` command. Configuration options for
 some Logstash plugins have changed in the 2.0 release.
 5. Restart your Logstash pipeline after updating your configuration file.
 
@@ -28,7 +28,7 @@ This procedure downloads the relevant Logstash binaries directly from Elastic.
 1. Shut down your Logstash pipeline, including any inputs that send events to Logstash.
 2. Download the https://www.elastic.co/downloads/logstash[Logstash installation file] that matches your host environment.
 3. Unpack the installation file into your Logstash directory.
-4. Test your configuration file with the `logstash --configtest -f <configuration-file>` command. Configuration options for
+4. Test your configuration file with the `logstash --config.test_and_exit -f <configuration-file>` command. Configuration options for
 some Logstash plugins have changed in the 2.0 release.
 5. Restart your Logstash pipeline after updating your configuration file.
 
@@ -91,8 +91,8 @@ The default batch size of the pipeline is 125 events per worker. This will by de
 used for the elasticsearch output. The Elasticsearch output's `flush_size` now acts only as a maximum bulk
 size (still defaulting to 500). For example, if your pipeline batch size is 3000 events, Elasticsearch
 Output will send 500 events at a time, in 6 separate bulk requests. In other words, for Elasticsearch output,
-bulk request size is chunked based on `flush_size` and `--pipeline-batch-size`. If `flush_size` is set greater
-than `--pipeline-batch-size`, it is ignored and `--pipeline-batch-size` will be used.
+bulk request size is chunked based on `flush_size` and `--pipeline.batch.size`. If `flush_size` is set greater
+than `--pipeline.batch.size`, it is ignored and `--pipeline.batch.size` will be used.
 
 The default number of output workers in Logstash 2.2 is now equal to the number of pipeline workers (`-w`)
 unless overridden in the Logstash config file. This can be problematic for some users as the