Reorg docs a bit.

PennLINC · Jan 31, 2024 · ac9450d · ac9450d
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diff --git a/docs/cli.rst b/docs/cli.rst
@@ -0,0 +1,14 @@
+======================
+Command Line Interface
+======================
+
+.. code-block:: bash
+
+	cubids --help
+
+This will print the instructions for using the command line interface in your command line.
+
+.. argparse::
+   :ref: cubids.cli._get_parser
+   :prog: cubids
+   :func: _get_parser
diff --git a/docs/glossary.rst b/docs/glossary.rst
@@ -1,5 +1,8 @@
 .. include:: links.rst
 
+Glossary
+========
+
 .. glossary::
 
     Key Group
@@ -32,6 +35,6 @@
 
 
 References
-==========
+----------
 
 .. footbibliography::
diff --git a/docs/index.rst b/docs/index.rst
@@ -9,8 +9,9 @@ Contents
    :maxdepth: 2
 
    about
-   usage
    installation
+   usage
+   cli
    example
    examples
    ../CONTRIBUTING

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -1,6 +1,6 @@
-==================
-Commands & Actions
-==================
+========================
+General Usage Guidelines
+========================
 
 Before we implement a ``CuBIDS`` workflow, let's define the terminology
 and take a look at some of the commands available in the software.
@@ -226,25 +226,9 @@ Applying these changes we would see:
     :header-rows: 1
 
 
-Command line tools
-------------------
-
-With that brief introduction done, we can introduce the full gamut of ``CuBIDS`` command line tools:
-
-.. code-block:: bash
-
-	cubids --help
-
-This will print the instructions for using the command line interface in your command line.
-
-.. argparse::
-   :ref: cubids.cli._get_parser
-   :prog: cubids
-   :func: _get_parser
-
-
 Customizable configuration
----------------------------
+--------------------------
+
 ``CuBIDS`` also features an optional, customizable, MRI image type-specific configuration file.
 This file can be passed as an argument to ``cubids group`` and ``cubids apply``
 using the ``--config`` flag and allows users to customize grouping settings based on