Incorporate doc updates from elastic/beats#6184

docs/copied-from-beats/command-reference.asciidoc

@@ -19,7 +19,15 @@
 :keystore-command-short-desc: Manages the <<keystore,secrets keystore>>
 :modules-command-short-desc: Manages configured modules
 :run-command-short-desc: Runs {beatname_uc}. This command is used by default if you start {beatname_uc} without specifying a command
+
+ifeval::["{has_ml_jobs}"=="yes"]
 :setup-command-short-desc: Sets up the initial environment, including the index template, Kibana dashboards (when available), and machine learning jobs (when available)
+endif::[]
+
+ifeval::["{has_ml_jobs}"!="yes"]
+:setup-command-short-desc: Sets up the initial environment, including the index template, Kibana dashboards (when available)
+endif::[]
+
 :test-command-short-desc: Tests the configuration
 :version-command-short-desc: Shows information about the current version
 
@@ -31,7 +39,7 @@
 <titleabbrev>Command reference</titleabbrev>
 ++++
 
-{beatname_uc} provides a command-line interface for running the Beat and
+{beatname_uc} provides a command-line interface for starting {beatname_uc} and
 performing common tasks, like testing configuration files and loading
 dashboards. The command-line also supports <<global-flags,global flags>>
 for controlling global behaviors.
@@ -164,7 +172,7 @@ Specifies the name of the command to show help for.
 [[keystore-command]]
 ==== `keystore` command
 
-{keystore-command-short-desc}. 
+{keystore-command-short-desc}.
 
 *SYNOPSIS*
 

docs/copied-from-beats/keystore.asciidoc

@@ -13,30 +13,33 @@
 === Secrets keystore
 
 When you configure {beatname_uc}, you might need to specify sensitive settings,
-such as passwords. Relying on the file system to protect these values is not
-sufficient. {beatname_uc} provides a keystore for storing secret values to use
-in configuration settings.
+such as passwords. Rather than relying on file system permissions to protect
+these values, you can use the {beatname_uc} keystore to securely store secret
+values for use in configuration settings.
 
-Unlike the Elasticsearch keystore, the {beatname_uc} keystore does not store
-actual configuration settings. Instead, you add a key and secret value to the
-keystore, and then use the key in place of the secret value when you configure
-sensitive settings.
+After adding a key and its secret value to the keystore, you can use the key in
+place of the secret value when you configure sensitive settings.
 
 The syntax for referencing keys is identical to the syntax for environment
 variables:
 
 `${KEY}`
 
-Where KEY is the name of the key. 
+Where KEY is the name of the key.
 
 For example, imagine that the keystore contains a key called `ES_PWD` with the
 value `yourelasticsearchpassword`:
 
 * In the configuration file, use `output.elasticsearch.password: "${ES_PWD}"`
-* On the command line, use: `-E "output.elasticsearch.password=${ES_PWD}"` 
+* On the command line, use: `-E "output.elasticsearch.password=${ES_PWD}"`
 
 When {beatname_uc} unpacks the configuration, it resolves keys before resolving
-environment variables and other variables.  
+environment variables and other variables.
+
+Notice that the {beatname_uc} keystore differs from the Elasticsearch keystore.
+Whereas the Elasticsearch keystore lets you store `elasticsearch.yml` values by
+name, the {beatname_uc} keystore lets you specify arbitrary names that you can
+reference in the {beatname_uc} configuration.
 
 To create and manage keys, use the `keystore` command. See the
 <<keystore-command,command reference>> for the full command syntax, including