further changes following review

docs/codeql/codeql-cli/codeql-cli-reference/about-ql-packs.rst

@@ -145,7 +145,7 @@ the CodeQL repository.
 
    When you create a custom QL pack, it's usually a good idea to add it to the search path in your CodeQL configuration.
    This will ensure that any libraries the pack contains are available to the CodeQL CLI.
-   For more information, see ":doc:`Specifying command options in a CodeQL configuration file <../codeql-cli-reference/specifying-command-options-in-a-codeql-configuration-file>`."
+   For more information, see ":ref:`Specifying command options in a CodeQL configuration file <specifying-command-options-in-a-codeql-configuration-file>`."
 
 QL packs for custom test files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

docs/codeql/codeql-cli/codeql-cli-reference/index.rst

@@ -12,7 +12,6 @@ Learn more about the files you can use when running CodeQL processes and the res
    about-ql-packs
    query-reference-files
    sarif-output
-   specifying-command-options-in-a-codeql-configuration-file
    exit-codes
 
 
@@ -20,15 +19,13 @@ Learn more about the files you can use when running CodeQL processes and the res
   contain queries, library files, query suites, and important metadata. 
 - :doc:`Query reference files <query-reference-files>`: A query reference file is text file that defines the location of one query to test.
 - :doc:`SARIF output <sarif-output>`: CodeQL supports SARIF as an output format for sharing static analysis results.
-- :doc:`Specifying command options in a CodeQL configuration file <specifying-command-options-in-a-codeql-configuration-file>`: 
-  You can save default or frequently used options for your commands in a per-user configuration file.
 - :doc:`Exit codes <exit-codes>`: The CodeQL CLI reports the status of each command it runs as an exit code.
   This exit code provides information for subsequent commands or for other tools that rely on the CodeQL CLI.
 
 .. _cli-commands:
 
-CodeQL CLI commands
--------------------
+CodeQL CLI manual
+-----------------
 
 To view provide detailed information about each CodeQL CLI command,
 including its usage and options, visit the "`CodeQL CLI manual <../codeql-cli-manual>`__."

docs/codeql/codeql-cli/codeql-cli-reference/query-reference-files.rst

@@ -40,7 +40,7 @@ A query reference file to test a JavaScript alert query:
 The `QL pack <https://github.com/github/codeql/blob/main/javascript/ql/test/qlpack.yml>`__ 
 for the ``javascript/ql/test`` directory defines the ``codeql-javascript`` queries as
 a dependency. So the query reference file defines the location of the query relative
-to the ``codeql-javascript`` QL pack:
+to the ``codeql-javascript`` QL pack::
 
     AngularJS/DeadAngularJSEventListener.ql
 

docs/codeql/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli.rst

@@ -184,7 +184,7 @@ executable in a couple of ways:
   can run the executable as just ``codeql``. 
 
 At this point, you can execute CodeQL commands. For a full list of the CodeQL
-CLI commands, see the ":ref:`CodeQL CLI reference <codeql-cli-reference>`."
+CLI commands, see the "`CodeQL CLI manual <../../codeql-cli-manual>`__."
 
 .. pull-quote:: Note
 

docs/codeql/codeql-cli/using-the-codeql-cli/index.rst

@@ -41,6 +41,9 @@ See the following links to learn how to get set up and run CodeQL commands:
   Test query help files by rendering them as markdown to ensure they are valid 
   before uploading them to the CodeQL repository or using them in code scanning.
 
+- :doc:`Specifying command options in a CodeQL configuration file <specifying-command-options-in-a-codeql-configuration-file>`: 
+  You can save default or frequently used options for your commands in a per-user configuration file.
+
 .. toctree::
    :titlesonly:
    :hidden:
@@ -53,4 +56,5 @@ See the following links to learn how to get set up and run CodeQL commands:
    using-custom-queries-with-the-codeql-cli
    creating-codeql-query-suites
    testing-custom-queries
-   testing-query-help-files
+   testing-query-help-files
+   Specifying command options <specifying-command-options-in-a-codeql-configuration-file>

docs/codeql/codeql-cli/using-the-codeql-cli/testing-custom-queries.rst

@@ -231,7 +231,7 @@ When the test runs it:
    ``codeql test run --search-path=java java/tests/EmptyThen``
 
    For information about saving the search path as part of your configuration, see
-   ":doc:`Specifying command options in a CodeQL configuration file <../codeql-cli-reference/specifying-command-options-in-a-codeql-configuration-file>`."
+   ":ref:`Specifying command options in a CodeQL configuration file <specifying-command-options-in-a-codeql-configuration-file>`."
 #. Executes the test by running the query and generating an ``EmptyThen.actual`` results file.
 #. Checks for an ``EmptyThen.expected`` file to compare with the ``.actual`` results file.
 #. Reports the results of the test --- in this case, a failure: ``0 tests passed; 1 tests failed:``.