Add tocs with links to deprecated articles

Author: saritai

docs/codeql/codeql-cli/about-codeql-packs.rst

@@ -6,4 +6,20 @@ About CodeQL packs
 .. pull-quote:: 
   This article was moved to "`About CodeQL packs <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `CodeQL pack structure <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#codeql-pack-structure>`__
+    * `About published packs <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#about-published-packs>`__
+* `About qlpack.yml files <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#about-qlpackyml-files>`__
+    * `qlpack.yml properties <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#qlpackyml-properties>`__
+* `About codeql-pack.lock.yml files <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#about-codeql-packlockyml-files>`__
+* `Examples of custom CodeQL packs <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#examples-of-custom-codeql-packs>`__
+    * `CodeQL packs for custom libraries <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#codeql-packs-for-custom-libraries>`__
+    * `CodeQL packs for custom queries <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#codeql-packs-for-custom-queries>`__
+    * `CodeQL packs for custom tests <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#codeql-packs-for-custom-tests>`__
+* `Examples of CodeQL packs in the CodeQL repository <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#examples-of-codeql-packs-in-the-codeql-repository>`__
+    * `Core library pack <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#core-library-pack>`__
+    * `Core query pack <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#core-query-pack>`__
+    * `Tests for the core CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-packs#tests-for-the-core-codeql-pack>`__

docs/codeql/codeql-cli/about-codeql-workspaces.rst

@@ -7,4 +7,10 @@ About CodeQL workspaces
   This article was moved to "`About CodeQL workspaces <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-workspaces>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
   .. include:: ../reusables/codeql-cli-articles-migration-note.rst
-  
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `The codeql-workspace.yml file <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-workspaces#the-codeql-workspaceyml-file>`__
+* `Source dependencies <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-workspaces#source-dependencies>`__
+* `CodeQL workspaces and query resolution <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-workspaces#codeql-workspaces-and-query-resolution>`__
+    * `Example <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/about-codeql-workspaces#example>`__

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

@@ -6,4 +6,8 @@ About the CodeQL CLI
 .. pull-quote:: 
   This article was moved to "`About the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/about-the-codeql-cli>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `CodeQL CLI commands <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/about-the-codeql-cli#codeql-cli-commands>`__

docs/codeql/codeql-cli/analyzing-databases-with-the-codeql-cli.rst

@@ -6,4 +6,20 @@ Analyzing databases with the CodeQL CLI
 .. pull-quote:: 
   This article was moved to "`Analyzing databases with the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `Running codeql database analyze <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#running-codeql-database-analyze>`__
+* `Specifying which queries to run in a CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#specifying-which-queries-to-run-in-a-codeql-pack>`__
+    * `Example query specifiers <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#example-query-specifiers>`__
+* `Examples of running database analyses <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#examples-of-running-database-analyses>`__
+    * `Running a CodeQL query pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#running-a-codeql-query-pack>`__
+    * `Running a single query <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#running-a-single-query>`__
+    * `Running all queries in a directory <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#running-all-queries-in-a-directory>`__
+    * `Running a subset of queries in a CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#running-a-subset-of-queries-in-a-codeql-pack>`__
+    * `Running query suites <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#running-query-suites>`__
+        * `Diagnostic and summary information <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#diagnostic-and-summary-information>`__
+    * `Integrating a CodeQL pack into a code scanning workflow in GitHub <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#integrating-a-codeql-pack-into-a-code-scanning-workflow-in-github>`__
+    * `Including query help for custom CodeQL queries in SARIF files <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#including-query-help-for-custom-codeql-queries-in-sarif-files>`__
+* `Results <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/analyzing-databases-with-the-codeql-cli#results>`__

docs/codeql/codeql-cli/creating-and-working-with-codeql-packs.rst

@@ -6,4 +6,12 @@ Creating and working with CodeQL packs
 .. pull-quote:: 
   This article was moved to "`Creating and working with CodeQL packs <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-and-working-with-codeql-packs>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `About CodeQL packs and the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-and-working-with-codeql-packs#about-codeql-packs-and-the-codeql-cli>`__
+* `Creating a CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-and-working-with-codeql-packs#creating-a-codeql-pack>`__
+* `Modifying an existing legacy QL pack to create a CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-and-working-with-codeql-packs#modifying-an-existing-legacy-ql-pack-to-create-a-codeql-pack>`__
+* `Adding and installing dependencies to a CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-and-working-with-codeql-packs#adding-and-installing-dependencies-to-a-codeql-pack>`__
+* `Customizing a downloaded CodeQL pack <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-and-working-with-codeql-packs#customizing-a-downloaded-codeql-pack>`__

docs/codeql/codeql-cli/creating-codeql-databases.rst

@@ -6,4 +6,19 @@ Creating CodeQL databases
 .. pull-quote:: 
   This article was moved to "`Creating CodeQL databases <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `Running codeql database create <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#running-codeql-database-create>`__
+* `Progress and results <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#progress-and-results>`__
+* `Creating databases for non-compiled languages <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#creating-databases-for-non-compiled-languages>`__
+      * `JavaScript and TypeScript <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#javascript-and-typescript>`__
+      * `Python <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#python>`__
+      * `Ruby <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#ruby>`__
+* `Creating databases for compiled languages <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#creating-databases-for-compiled-languages>`__
+    * `Detecting the build system <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#detecting-the-build-system>`__
+    * `Specifying build commands <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#specifying-build-commands>`__
+    * `Using indirect build tracing <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#using-indirect-build-tracing>`__
+    * `Example of creating a CodeQL database using indirect build tracing <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#example-of-creating-a-codeql-database-using-indirect-build-tracing>`__
+* `Downloading databases from GitHub.com <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-databases#downloading-databases-from-githubcom>`__

docs/codeql/codeql-cli/creating-codeql-query-suites.rst

@@ -6,4 +6,16 @@ Creating CodeQL query suites
 .. pull-quote:: 
   This article was moved to "`Creating CodeQL query suites <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `Locating queries to add to a query suite <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#locating-queries-to-add-to-a-query-suite>`__
+* `Filtering the queries in a query suite <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#filtering-the-queries-in-a-query-suite>`__
+    * `Examples of filtering which queries are run <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#examples-of-filtering-which-queries-are-run>`__
+* `Reusing existing query suite definitions <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#reusing-existing-query-suite-definitions>`__
+    * `Reusability Examples <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#reusability-examples>`__
+* `Naming a query suite <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#naming-a-query-suite>`__
+* `Saving a query suite <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#saving-a-query-suite>`__
+* `Specifying well-known query suites <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#specifying-well-known-query-suites>`__ 
+* `Using query suites with CodeQL <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/creating-codeql-query-suites#using-query-suites-with-codeql>`__  

docs/codeql/codeql-cli/exit-codes.rst

@@ -6,4 +6,4 @@ Exit codes
 .. pull-quote:: 
   This article was moved to "`Exit codes <https://docs.github.com/en/code-security/codeql-cli/codeql-cli-reference/exit-codes>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst

docs/codeql/codeql-cli/extractor-options.rst

@@ -6,4 +6,10 @@ Extractor options
 .. pull-quote:: 
   This article was moved to "`Extractor options <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/extractor-options>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `About extractor options <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/extractor-options#about-extractor-options>`__
+* `Setting extractor options with the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/extractor-options#setting-extractor-options-with-the-codeql-cli>`__
+* `Setting extractor options from files <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/extractor-options#setting-extractor-options-from-files>`__

docs/codeql/codeql-cli/getting-started-with-the-codeql-cli.rst

@@ -6,4 +6,20 @@ Getting started with the CodeQL CLI
 .. pull-quote:: 
   This article was moved to "`Getting started with the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli>`__" on the `GitHub Docs <https://docs.github.com/en/code-security/codeql-cli>`__ site as of January 2023.
 
-  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+  .. include:: ../reusables/codeql-cli-articles-migration-note.rst
+
+.. include:: ../reusables/codeql-cli-migration-toc-note.rst
+
+* `Setting up the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#setting-up-the-codeql-cli>`__
+    * `1. Download the CodeQL CLI zip package <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#1-download-the-codeql-cli-zip-package>`__
+    * `2. Extract the zip archive <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#2-extract-the-zip-archive>`__
+    * `3. Launch codeql <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#3-launch-codeql>`__
+    * `4. Verify your CodeQL CLI setup <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#4-verify-your-codeql-cli-setup>`__
+* `Checking out the CodeQL source code directly <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#checking-out-the-codeql-source-code-directly>`__
+    * `1. Download the CodeQL CLI zip <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#1-download-the-codeql-cli-zip>`__
+    * `2. Create a new CodeQL directory <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#2-create-a-new-codeql-directory>`__
+    * `3. Obtain a local copy of the CodeQL queries <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#3-obtain-a-local-copy-of-the-codeql-queries>`__
+    * `4. Extract the zip archive <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#4-extract-the-zip-archive>`__
+    * `5. Launch codeql <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#5-launch-codeql>`__
+    * `6. Verify your CodeQL CLI setup <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#6-verify-your-codeql-cli-setup>`__
+* `Using two versions of the CodeQL CLI <https://docs.github.com/en/code-security/codeql-cli/using-the-codeql-cli/getting-started-with-the-codeql-cli#using-two-versions-of-the-codeql-cli>`__