[DOCS] Refactor book-scoped variables in docs/reference/index.asciidoc (#107413)

* Remove `es-test-dir` book-scoped variable

* Remove `plugins-examples-dir` book-scoped variable

* Remove `:dependencies-dir:` and `:xes-repo-dir:` book-scoped variables

- In `index.asciidoc`, two variables (`:dependencies-dir:` and `:xes-repo-dir:`) were removed.
- In `sql/index.asciidoc`, the `:sql-tests:` path was updated to fuller path
- In `esql/index.asciidoc`, the `:esql-tests:` path was updated idem

* Replace `es-repo-dir` with `es-ref-dir`

* Move `:include-xpack: true` to few files that use it, remove from index.asciidoc

docs/reference/scripting/apis/create-stored-script-api.asciidoc

@@ -67,7 +67,7 @@ the API immediately compiles the script or template in this context.
 If you specify both this and the `<context>` request path parameter, the API
 uses the request path parameter.
 
-include::{es-repo-dir}/rest-api/common-parms.asciidoc[tag=timeoutparms]
+include::{es-ref-dir}/rest-api/common-parms.asciidoc[tag=timeoutparms]
 
 [role="child_attributes"]
 [[create-stored-script-api-request-body]]

docs/reference/scripting/apis/delete-stored-script-api.asciidoc

@@ -47,4 +47,4 @@ Identifier for the stored script or search template.
 [[delete-stored-script-api-query-params]]
 ==== {api-query-parms-title}
 
-include::{es-repo-dir}/rest-api/common-parms.asciidoc[tag=timeoutparms]
+include::{es-ref-dir}/rest-api/common-parms.asciidoc[tag=timeoutparms]

docs/reference/scripting/apis/get-stored-script-api.asciidoc

@@ -55,4 +55,4 @@ Identifier for the stored script or search template.
 [[get-stored-script-api-query-params]]
 ==== {api-query-parms-title}
 
-include::{es-repo-dir}/rest-api/common-parms.asciidoc[tag=master-timeout]
+include::{es-ref-dir}/rest-api/common-parms.asciidoc[tag=master-timeout]

docs/reference/scripting/engine.asciidoc

@@ -17,7 +17,7 @@ the document frequency of a provided term.
 
 ["source","java",subs="attributes,callouts,macros"]
 --------------------------------------------------
-include-tagged::{plugins-examples-dir}/script-expert-scoring/src/main/java/org/elasticsearch/example/expertscript/ExpertScriptPlugin.java[expert_engine]
+include-tagged::{elasticsearch-root}/plugins/examples/script-expert-scoring/src/main/java/org/elasticsearch/example/expertscript/ExpertScriptPlugin.java[expert_engine]
 --------------------------------------------------
 
 You can execute the script by specifying its `lang` as `expert_scripts`, and the name