Update CodeQL CLI manual (#57358)

Co-authored-by: mc <42146119+mchammer01@users.noreply.github.com>

Author: docs-bot

content/code-security/codeql-cli/codeql-cli-manual/generate-overlay-changes.md

@@ -0,0 +1,101 @@
+---
+title: generate overlay-changes
+intro: |
+  [Plumbing] Generate a file that can be used for the
+versions: # DO NOT MANUALLY EDIT. CHANGES WILL BE OVERWRITTEN BY A 🤖
+  fpt: '*'
+  ghec: '*'
+  ghes: '*'
+topics:
+  - Code Security
+  - Code scanning
+  - CodeQL
+type: reference
+product: '{% data reusables.gated-features.codeql %}'
+autogenerated: codeql-cli
+---
+
+<!-- Content after this section is automatically generated -->
+
+{% data reusables.codeql-cli.man-pages-version-note %}
+
+## Synopsis
+
+```shell copy
+codeql generate overlay-changes [--source-root=<dir>] [--output=<file>] <options>... -- <database>
+```
+
+## Description
+
+\[Plumbing] Generate a file that can be used for the
+`--overlay-changes` option to
+[codeql database create](/code-security/codeql-cli/codeql-cli-manual/database-create) when extracting an overlay database.
+
+This command is intended to be used mostly for manual or automated
+testing. It is not particularly efficient. For production use, consider
+if the changes file can instead be derived from something like
+`git diff --name-only`.
+
+## Options
+
+### Primary Options
+
+#### `<database>`
+
+\[Mandatory] Path to the _base_ database into which the overlay will be
+extracted.
+
+#### `-s, --source-root=<dir>`
+
+The directory containing the source code to be extracted as an overlay.
+If not given, the current working directory is used.
+
+#### `-o, --output=<file>`
+
+The changes file will be written to this location. If it is not
+specified, the changes will be written to standard output.
+
+### Common options
+
+#### `-h, --help`
+
+Show this help text.
+
+#### `-J=<opt>`
+
+\[Advanced] Give option to the JVM running the command.
+
+(Beware that options containing spaces will not be handled correctly.)
+
+#### `-v, --verbose`
+
+Incrementally increase the number of progress messages printed.
+
+#### `-q, --quiet`
+
+Incrementally decrease the number of progress messages printed.
+
+#### `--verbosity=<level>`
+
+\[Advanced] Explicitly set the verbosity level to one of errors,
+warnings, progress, progress+, progress++, progress+++. Overrides `-v`
+and `-q`.
+
+#### `--logdir=<dir>`
+
+\[Advanced] Write detailed logs to one or more files in the given
+directory, with generated names that include timestamps and the name of
+the running subcommand.
+
+(To write a log file with a name you have full control over, instead
+give `--log-to-stderr` and redirect stderr as desired.)
+
+#### `--common-caches=<dir>`
+
+\[Advanced] Controls the location of cached data on disk that will
+persist between several runs of the CLI, such as downloaded QL packs and
+compiled query plans. If not set explicitly, this defaults to a
+directory named `.codeql` in the user's home directory; it will be
+created if it doesn't already exist.
+
+Available since `v2.15.2`.

content/code-security/codeql-cli/codeql-cli-manual/index.md

@@ -55,6 +55,7 @@ children:
   - /execute-upgrades
   - /generate-extensible-predicate-metadata
   - /generate-log-summary
+  - /generate-overlay-changes
   - /generate-query-help
   - /github-merge-results
   - /github-upload-results

content/code-security/codeql-cli/codeql-cli-manual/resolve-languages.md

@@ -61,6 +61,12 @@ per-user configuration file).
 
 (Note: On Windows the path separator is `;`).
 
+#### `--[no-]filter-to-languages-with-queries`
+
+List only languages that have default queries.
+
+Available since `v2.23.0`.
+
 #### `--format=<fmt>`
 
 Select output format. Choices include:

content/code-security/codeql-cli/codeql-cli-manual/test-extract.md

@@ -27,7 +27,7 @@ redirect_from:
 ## Synopsis
 
 ```shell copy
-codeql test extract [--source-root=<dir>] <options>... -- <testDirectory>
+codeql test extract [--print-database] [--source-root=<dir>] <options>... -- <testDirectory>
 ```
 
 ## Description
@@ -52,6 +52,11 @@ Override the location of the database being created. By default it will
 be a subdirectory whose name is derived from the name of the test
 directory itself with '.testproj' appended.
 
+#### `-D, --print-database`
+
+Print the path to the database being created, rather than the dataset
+inside it.
+
 #### `-s, --source-root=<dir>`
 
 \[Advanced] The root source code directory, if different from the test