update links to codeql cli manual

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

@@ -26,4 +26,4 @@ command line. To run a command, use::
    codeql [command] [subcommand]
 
 To view the reference documentation for a command, add the ``--help`` flag, or visit the 
-"`CodeQL CLI manual <../../codeql-cli-manual>`__."
+"`CodeQL CLI manual <../manual>`__."

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

@@ -49,7 +49,7 @@ You must specify:
   <sarif-file>`, and graph formats. For more information about CSV and SARIF,
   see `Results <#results>`__. To find out which other results formats are
   supported, see the `database analyze reference
-  <../codeql-cli-manual/database-analyze.html>`__.
+  <../manual/database-analyze>`__.
 
 - ``--output``: the output path of the results file generated during analysis.
 
@@ -70,7 +70,7 @@ You can also specify:
    <upgrading-codeql-databases>`."
 
 For full details of all the options you can use when analyzing databases, see
-the `database analyze reference documentation <../codeql-cli-manual/database-analyze.html>`__.
+the `database analyze reference documentation <../manual/database-analyze>`__.
 
 .. _database-analyze-examples:
 

docs/codeql/codeql-cli/codeql-cli-reference.rst

@@ -28,4 +28,4 @@ CodeQL CLI manual
 -----------------
 
 To view detailed information about each CodeQL CLI command,
-including its usage and options, add the ``--help`` flag or visit the "`CodeQL CLI manual <../codeql-cli-manual>`__."
+including its usage and options, add the ``--help`` flag or visit the "`CodeQL CLI manual <../manual>`__."

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

@@ -50,7 +50,7 @@ the language you want to analyze:
   detect the build system automatically, using a built-in autobuilder. 
    
 For full details of all the options you can use when creating databases,
-see the `database create reference documentation <../codeql-cli-manual/database-create.html>`__.  
+see the `database create reference documentation <../manual/database-create>`__.  
 
 Progress and results
 --------------------

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

@@ -234,7 +234,7 @@ instruction::
    - description: <name-of-query-suite>
 
 This value is displayed when you run `codeql resolve queries
-<../codeql-cli-manual/resolve-queries.html>`__, if the suite is added to a "well-known"
+<../manual/resolve-queries>`__, if the suite is added to a "well-known"
 directory. For more information, see "`Specifying well-known query suites
 <#specifying-well-known-query-suites>`__." 
 

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

@@ -16,7 +16,7 @@ Success, normal termination.
 
 The command successfully determined that the answer to your question is "no".
 
-This exit code is only used by a few commands, such as `codeql test run <../codeql-cli-manual/test-run.html>`__, `codeql database check <../codeql-cli-manual/dataset-check.html>`__, `codeql query format <../codeql-cli-manual/query-format.html>`__,and `codeql resolve extractor <../codeql-cli-manual/resolve-extractor.html>`__.
+This exit code is only used by a few commands, such as `codeql test run <../manual/test-run>`__, `codeql database check <../manual/dataset-check>`__, `codeql query format <../manual/query-format>`__,and `codeql resolve extractor <../manual/resolve-extractor>`__.
 For more details, see the documentation for those commands.
 
 2
@@ -37,7 +37,7 @@ In this case, the launcher can't start the Java code for the CodeQL CLI at all.
 32
 ---
 
-The extractor didn't find any code to analyze when running `codeql database create <../codeql-cli-manual/database-create.html>`__ or `codeql database finalize <../codeql-cli-manual/database-finalize.html>`__.
+The extractor didn't find any code to analyze when running `codeql database create <../manual/database-create>`__ or `codeql database finalize <../manual/database-finalize>`__.
 
 33
 ---

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

@@ -184,7 +184,7 @@ executable in a couple of ways:
   can run the executable as just ``codeql``. 
 
 At this point, you can execute CodeQL commands. For a full list of the CodeQL
-CLI commands, see the "`CodeQL CLI manual <../../codeql-cli-manual>`__."
+CLI commands, see the "`CodeQL CLI manual <../manual>`__."
 
 .. pull-quote:: Note
 

docs/codeql/codeql-cli/index.rst

@@ -10,7 +10,7 @@ CodeQL CLI
 
 - :ref:`CodeQL CLI reference <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 <../codeql-cli-manual>`__: Detailed information about all the commands available with the CodeQL CLI.
+- `CodeQL CLI manual <manual>`__: Detailed information about all the commands available with the CodeQL CLI.
 
 .. toctree::
    :titlesonly:

docs/codeql/codeql-cli/sarif-output.rst

@@ -11,7 +11,7 @@ considered "optional". This document details the output produced when using the
 format type ``sarifv2.1.0``, which corresponds to the SARIF v2.1.0.csd1
 specification.
 For more information on selecting a file format for your analysis results, see
-the `database analyze reference <../codeql-cli-manual/database-analyze.html>`__.
+the `database analyze reference <../manual/database-analyze>`__.
 
 SARIF specification and schema
 ------------------------------

docs/codeql/codeql-cli/testing-custom-queries.rst

@@ -130,7 +130,7 @@ You can also specify:
 - .. include:: ../reusables/threads-query-execution.rst
 
 For full details of all the options you can use when testing queries,
-see the `test run reference documentation <../codeql-cli-manual/test-run.html>`__.
+see the `test run reference documentation <../manual/test-run>`__.
 
 Example
 -------

docs/codeql/codeql-cli/testing-query-help-files.rst

@@ -54,7 +54,7 @@ The ``--output`` option defines a file path where the rendered query help will b
 
 For full details of all the options you can use when testing query help files,
 see the `generate query-help reference documentation
-<codeql-cli-manual:generate-query-help>`__.
+<../manual/generate-query-help>`__.
 
 Results
 -------
@@ -73,7 +73,7 @@ By default, the CodeQL CLI will print a warning message if:
   as an accompanying ``.qhelp`` file
 
 You can tell the CodeQL CLI how to handle these warnings by including a ``--warnings`` option in your command.
-For more information, see the `generate query-help reference documentation <../codeql-cli-manual/generate-query-help.html#cmdoption-codeql-generate-query-help-warnings>`__.
+For more information, see the `generate query-help reference documentation <../manual/generate-query-help#cmdoption-codeql-generate-query-help-warnings>`__.
 
 Further reading
 ---------------

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

@@ -40,7 +40,7 @@ where ``<database>``, the path to the CodeQL database you
 want to upgrade, must be specified.
 
 For full details of all the options you can use when upgrading databases,
-see the "`database upgrade <../codeql-cli-manual/database-upgrade.html>`__"  reference documentation.
+see the "`database upgrade <../manual/database-upgrade>`__"  reference documentation.
 
 Progress and results
 --------------------

docs/codeql/codeql-cli/using-custom-queries-with-the-codeql-cli.rst

@@ -7,7 +7,7 @@ You can customize your CodeQL analyses by writing your own queries to highlight
 specific vulnerabilities or errors.
 
 This topic is specifically about writing
-queries to use with the `database analyze <../codeql-cli-manual/database-analyze.html>`__
+queries to use with the `database analyze <../manual/database-analyze>`__
 command to produce :ref:`interpreted results <interpret-query-results>`. 
 
 .. include:: ../reusables/advanced-query-execution.rst

docs/codeql/codeql-for-visual-studio-code/analyzing-your-projects.rst

@@ -137,7 +137,7 @@ 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/codeql-cli-manual/database-cleanup.html>`__ reference documentation.
+     For more information, see the `database cleanup <../../codeql-cli/manual/database-cleanup>`__ reference documentation.
 
 Comparing query results
 ------------------------

docs/codeql/reusables/advanced-query-execution.rst

@@ -4,15 +4,15 @@
    <including-query-metadata>`. You can also execute queries using the following
    plumbing-level subcommands:
    
-   - `database run-queries <../codeql-cli-manual/database-run-queries.html>`__, which
+   - `database run-queries <../manual/database-run-queries>`__, which
      outputs non-interpreted results in an intermediate binary format called
      :ref:`BQRS <bqrs-file>`.
-   - `query run <../codeql-cli-manual/query-run.html>`__, which will output BQRS files, or print
+   - `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 <../codeql-cli-manual/bqrs-decode.html>`__ plumbing
+   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.