Merge pull request github#12967 from github/felicitymay-9916-update-links

Update links to CodeQL manual in the codeql.github.com site

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
 --------------------------------------------------------