restructure codeql docs

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

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+.. _using-the-codeql-cli:
+
+Using the CodeQL CLI
+====================
+
+.. include:: ../reusables/codeql-cli-overview.rst
+
+See the following links to learn how to get set up and run CodeQL commands:
+
+- :doc:`About the CodeQL CLI <about-the-codeql-cli>`: Software 
+  developers and security researchers can secure their code using the CodeQL CLI.
+
+- :doc:`Getting started with the CodeQL CLI
+  <getting-started-with-the-codeql-cli>`: Set up the
+  CodeQL CLI so that you can run CodeQL processes from your command line.
+
+- :doc:`Creating CodeQL databases
+  <creating-codeql-databases>`: Create relational
+  representations of source code that can be queried like any other database.
+  
+- :doc:`Analyzing CodeQL databases with the CodeQL CLI
+  <analyzing-databases-with-the-codeql-cli>`: Analyze your code using queries
+  written in a specially-designed, object-oriented query language.
+
+- :doc:`Upgrading CodeQL databases
+  <upgrading-codeql-databases>`: Upgrade your databases so
+  that they can be analyzed using the most up to date CodeQL products.
+
+- :doc:`Using custom queries with the CodeQL CLI
+  <using-custom-queries-with-the-codeql-cli>`: Use custom queries to extend your
+  analysis or highlight errors that are specific to a particular codebase.
+
+- :doc:`Creating CodeQL query suites <creating-codeql-query-suites>`:
+  Define query suite definitions for groups of frequently used queries.
+
+- :doc:`Testing custom queries <testing-custom-queries>`: Set up
+  regression testing of custom queries to ensure that they behave as expected in
+  your analysis.
+
+- :doc:`Testing query help files <testing-query-help-files>`:
+  Test query help files by rendering them as markdown to ensure they are valid 
+  before adding 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:
+
+   about-the-codeql-cli
+   getting-started-with-the-codeql-cli
+   creating-codeql-databases
+   analyzing-databases-with-the-codeql-cli
+   upgrading-codeql-databases
+   using-custom-queries-with-the-codeql-cli
+   creating-codeql-query-suites
+   testing-custom-queries
+   testing-query-help-files
+   Specifying command options <specifying-command-options-in-a-codeql-configuration-file>