docs: Update "Advanced Setup" section

docs/integrations-index.asciidoc

@@ -64,6 +64,8 @@ include::apm-components.asciidoc[]
 
 include::apm-quick-start.asciidoc[]
 
+include::./legacy/setting-up-and-running.asciidoc[]
+
 include::data-model.asciidoc[]
 
 include::features.asciidoc[]
@@ -127,11 +129,6 @@ include::./legacy/overview.asciidoc[]
 
 include::./legacy/getting-started-apm-server.asciidoc[]
 
-include::./legacy/setting-up-and-running.asciidoc[]
-
-// TODO: This section needs to integrate above
-include::./legacy/data-ingestion.asciidoc[]
-
 :beat-specific-security: {docdir}/legacy/security.asciidoc
 include::{libbeat-dir}/shared-securing-beat.asciidoc[leveloffset=+1]
 

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

@@ -34,7 +34,6 @@ ifdef::serverless[]
 endif::serverless[]
 
 :help-command-short-desc: Shows help for any command
-:keystore-command-short-desc: Manages the <<keystore,secrets keystore>>
 :modules-command-short-desc: Manages configured modules
 :package-command-short-desc: Packages the configuration and executable into a zip file
 :remove-command-short-desc: Removes the specified function from your serverless environment
@@ -65,6 +64,8 @@ endif::[]
 <titleabbrev>Command reference</titleabbrev>
 ++++
 
+IMPORTANT: These commands only apply to the APM Server binary installation method.
+
 ifndef::no_dashboards[]
 {beatname_uc} provides a command-line interface for starting {beatname_uc} and
 performing common tasks, like testing configuration files and loading dashboards.
@@ -105,9 +106,6 @@ ifdef::apm-server[]
 endif::[]
 |<<export-command,`export`>> |{export-command-short-desc}.
 |<<help-command,`help`>> |{help-command-short-desc}.
-ifndef::serverless[]
-|<<keystore-command,`keystore`>> |{keystore-command-short-desc}.
-endif::[]
 ifeval::["{beatname_lc}"=="functionbeat"]
 |<<package-command,`package`>> |{package-command-short-desc}.
 |<<remove-command,`remove`>> |{remove-command-short-desc}.
@@ -432,65 +430,6 @@ Specifies the name of the command to show help for.
 {beatname_lc} help export
 -----
 
-ifndef::serverless[]
-[float]
-[[keystore-command]]
-==== `keystore` command
-
-{keystore-command-short-desc}.
-
-*SYNOPSIS*
-
-["source","sh",subs="attributes"]
-----
-{beatname_lc} keystore SUBCOMMAND [FLAGS]
-----
-
-*`SUBCOMMAND`*
-
-*`add KEY`*::
-Adds the specified key to the keystore. Use the `--force` flag to overwrite an
-existing key. Use the `--stdin` flag to pass the value through `stdin`.
-
-*`create`*::
-Creates a keystore to hold secrets. Use the `--force` flag to overwrite the
-existing keystore.
-
-*`list`*::
-Lists the keys in the keystore.
-
-*`remove KEY`*::
-Removes the specified key from the keystore.
-
-*FLAGS*
-
-*`--force`*::
-Valid with the `add` and `create` subcommands. When used with `add`, overwrites
-the specified key. When used with `create`, overwrites the keystore.
-
-*`--stdin`*::
-When used with `add`, uses the stdin as the source of the key's value.
-
-*`-h, --help`*::
-Shows help for the `keystore` command.
-
-
-{global-flags}
-
-*EXAMPLES*
-
-["source","sh",subs="attributes"]
------
-{beatname_lc} keystore create
-{beatname_lc} keystore add ES_PWD
-{beatname_lc} keystore remove ES_PWD
-{beatname_lc} keystore list
------
-
-See <<keystore>> for more examples.
-
-endif::[]
-
 ifeval::["{beatname_lc}"=="functionbeat"]
 [float]
 [[package-command]]

docs/legacy/copied-from-beats/docs/https.asciidoc

@@ -32,18 +32,10 @@ For example:
 output.elasticsearch:
   hosts: ["https://myEShost:9200"]
   username: "{beat_default_index_prefix}_writer" <1>
-  password: "{pwd}" <2>
+  password: "{pwd}"
 ----------------------------------------------------------------------
 <1> This user needs the privileges required to publish events to {es}.
 To create a user like this, see <<privileges-to-publish-events>>.
-<2> This example shows a hard-coded password, but you should store sensitive
-values
-ifndef::serverless[]
-in the <<keystore,secrets keystore>>.
-endif::[]
-ifdef::serverless[]
-in environment variables.
-endif::[]
 --
 
 * To use token-based *API key authentication*, specify the `api_key` under `output.elasticsearch`.
@@ -136,17 +128,9 @@ For example, specify a unique username and password to connect to {kib} like thi
 setup.kibana:
   host: "mykibanahost:5601"
   username: "{beat_default_index_prefix}_kib_setup" <1>
-  password: "{pwd}" <2>
+  password: "{pwd}"
 ----
 <1> This user needs privileges required to set up dashboards
-<2> This example shows a hard-coded password, but you should store sensitive
-values
-ifndef::serverless[]
-in the <<keystore,secrets keystore>>.
-endif::[]
-ifdef::serverless[]
-in environment variables.
-endif::[]
 endif::no_dashboards[]
 --