diff --git a/docs/codeql/codeql-cli/codeql-cli-reference.rst b/docs/codeql/codeql-cli/codeql-cli-reference.rst
index 458f833b1a1..2a58aece28b 100644
--- a/docs/codeql/codeql-cli/codeql-cli-reference.rst
+++ b/docs/codeql/codeql-cli/codeql-cli-reference.rst
@@ -1,5 +1,7 @@
 .. _codeql-cli-reference:
 
+:orphan:
+
 CodeQL CLI reference
 ====================
 
diff --git a/docs/codeql/codeql-cli/index.rst b/docs/codeql/codeql-cli/index.rst
index 721f7ed603e..b5a13f3425c 100644
--- a/docs/codeql/codeql-cli/index.rst
+++ b/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>
diff --git a/docs/codeql/codeql-cli/using-the-codeql-cli.rst b/docs/codeql/codeql-cli/using-the-codeql-cli.rst
index 0cc45536cec..2d60e8c2d12 100644
--- a/docs/codeql/codeql-cli/using-the-codeql-cli.rst
+++ b/docs/codeql/codeql-cli/using-the-codeql-cli.rst
@@ -1,5 +1,7 @@
 .. _using-the-codeql-cli:
 
+:orphan:
+
 Using the CodeQL CLI
 ====================
 
diff --git a/docs/codeql/codeql-for-visual-studio-code/analyzing-your-projects.rst b/docs/codeql/codeql-for-visual-studio-code/analyzing-your-projects.rst
index c3d1f15be6b..e69f82e4138 100644
--- a/docs/codeql/codeql-for-visual-studio-code/analyzing-your-projects.rst
+++ b/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
 ------------------------
diff --git a/docs/codeql/codeql-for-visual-studio-code/customizing-settings.rst b/docs/codeql/codeql-for-visual-studio-code/customizing-settings.rst
index fd384255c39..7cbe816cf1c 100644
--- a/docs/codeql/codeql-for-visual-studio-code/customizing-settings.rst
+++ b/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
 --------------------------------------------------------
diff --git a/docs/codeql/reusables/advanced-query-execution.rst b/docs/codeql/reusables/advanced-query-execution.rst
index b9466765d3a..c702f6d9d77 100644
--- a/docs/codeql/reusables/advanced-query-execution.rst
+++ b/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.
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