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
deleted file mode 100644
index b9466765d3a..00000000000
--- a/docs/codeql/reusables/advanced-query-execution.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-.. pull-quote:: Other query-running commands
-
-   Queries run with ``database analyze`` have strict `metadata requirements
-   <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
-     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
-     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
-   subcommand. Therefore, for most use cases it's easiest to use ``database
-   analyze`` to directly generate interpreted results.
\ No newline at end of file