Update links to CodeQL manual

Make CodeQL CLI a single item in the side navigation

Author: felicitymay

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

@@ -1,5 +1,7 @@
 .. _codeql-cli-reference:
 
+:orphan:
+
 CodeQL CLI reference
 ====================
 

docs/codeql/codeql-cli/index.rst

@@ -10,12 +10,9 @@ CodeQL CLI
 
 - `CodeQL CLI reference <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference>`__: Learn more about the files you can use when running CodeQL processes and the results format and exit codes that CodeQL generates.
 
-- `CodeQL CLI manual <manual>`__: Detailed information about all the commands available with the CodeQL CLI.
+- `CodeQL CLI manual <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-manual>`__: Detailed information about all the commands available with the CodeQL CLI.
 
 .. toctree::
    :titlesonly:
    :hidden:
 
-   using-the-codeql-cli
-   codeql-cli-reference
-   CodeQL CLI manual <https://codeql.github.com/docs/codeql-cli/manual>

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

@@ -1,5 +1,7 @@
 .. _using-the-codeql-cli:
 
+:orphan:
+
 Using the CodeQL CLI
 ====================
 

docs/codeql/codeql-for-visual-studio-code/analyzing-your-projects.rst

@@ -153,7 +153,7 @@ To use standard code navigation features in the source code, you can right-click
 
      If you're using an older database, code navigation commands such as **Go to Definition** and **Go to References** may not work.
      To use code navigation, try unzipping the database and running ``codeql database cleanup <database>`` on the unzipped database using the CodeQL CLI. Then, re-add the database to Visual Studio Code.
-     For more information, see the `database cleanup <../../codeql-cli/manual/database-cleanup>`__ reference documentation.
+     For more information, see `database cleanup <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-manual/database-cleanup>`__ in the documentation for CodeQL CLI.
 
 Comparing query results
 ------------------------

docs/codeql/codeql-for-visual-studio-code/customizing-settings.rst

@@ -112,7 +112,7 @@ Configuring settings for testing queries locally
 
 To increase the number of threads used for testing queries, you can update the **Running Tests > Number Of Threads** setting.
 
-To pass additional arguments to the CodeQL CLI when running tests, you can update the **Running Tests > Additional Test Arguments** setting. For more information about the available arguments, see "`test run <https://codeql.github.com/docs/codeql-cli/manual/test-run/>`_" in the CodeQL CLI help. 
+To pass additional arguments to the CodeQL CLI when running tests, you can update the **Running Tests > Additional Test Arguments** setting. For more information about the available arguments, see `test run <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-manual/test-run/>`_ in the documentation for CodeQL CLI. 
 
 Configuring settings for telemetry and data collection
 --------------------------------------------------------

docs/codeql/reusables/advanced-query-execution.rst

@@ -4,15 +4,15 @@
    <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/using-custom-queries-with-the-codeql-cli#including-query-metadata>`__. You can also execute queries using the following
    plumbing-level subcommands:
 
-   - `database run-queries <../manual/database-run-queries>`__, which
+   - `database run-queries <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-manual/database-run-queries>`__, which
      outputs non-interpreted results in an intermediate binary format called
      :ref:`BQRS <bqrs-file>`.
-   - `query run <../manual/query-run>`__, which will output BQRS files, or print
+   - `query run <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-manual/query-run>`__, which will output BQRS files, or print
      results tables directly to the command line. Viewing results directly in
      the command line may be useful for iterative query development using the CLI.
 
    Queries run with these commands don't have the same metadata requirements.
    However, to save human-readable data you have to process each BQRS results
-   file using the `bqrs decode <../manual/bqrs-decode>`__ plumbing
+   file using the `bqrs decode <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-manual/bqrs-decode>`__ plumbing
    subcommand. Therefore, for most use cases it's easiest to use ``database
    analyze`` to directly generate interpreted results.