Fixes build errors related to submodule (#322)

* Fixes build errors related to submodule

* Fixes more errors

* Copy review change

Author: sarahsimpers

source/atlas-cli-changelog.txt

@@ -861,6 +861,7 @@ including managing:
 - Alerts
 - Metrics and monitoring
 
-For a complete list of available commands, see :doc:`</command/atlas>`.
+For a complete list of available commands, see the 
+:ref:`{+atlas-cli+} commands <atlas>`.
 
 To install this version, see :ref:`<install-atlas-cli>`.

source/atlas-cli-tutorials.txt

@@ -18,8 +18,8 @@ Use the following tutorials to learn how to manage |service| using the
 To learn the {+atlas-cli+} basics, see :ref:`install-atlas-cli` and
 :ref:`connect-atlas-cli`.
 
-You can also go straight to the :doc:`{+atlas-cli+} Commands 
-</command/atlas>`.
+You can also go straight to the :ref:`{+atlas-cli+} Commands 
+<atlas>`.
 
 .. list-table:: 
    :header-rows: 1

source/connect-atlas-cli.txt

@@ -172,7 +172,7 @@ from the {+atlas-cli+}.
 
          .. step:: Issue commands using the ``--projectId`` and ``--orgId`` flags.
 
-            When you run :doc:`{+atlas-cli+} commands </command/atlas>` for
+            When you run :ref:`{+atlas-cli+} commands <atlas>` for
             the duration of your {+atlas-cli+} session, specify your Project ID and Org ID
             using the ``--projectId`` and ``--orgId`` flags.
 
@@ -206,7 +206,7 @@ from the {+atlas-cli+}.
 
          .. step:: Issue commands using the ``--projectId`` and ``--orgId`` flags.
 
-            When you run :doc:`{+atlas-cli+} commands </command/atlas>` for
+            When you run :ref:`{+atlas-cli+} commands <atlas>` for
             the duration of your {+atlas-cli+} session, specify your Project ID and Org ID
             using the ``--projectId`` and ``--orgId`` flags.
 
@@ -222,7 +222,7 @@ Take the Next Steps
 -------------------
 
 Start using the 
-:doc:`{+atlas-cli+} commands </command/atlas>`.
+:ref:`{+atlas-cli+} commands <atlas>`.
 
 To save connection settings by modifying the default profile or create a
 different profile, see :ref:`<atlas-cli-profiles>`.

source/install-atlas-cli.txt

@@ -631,7 +631,7 @@ Take the Next Steps
 -------------------
 
 :ref:`<connect-atlas-cli>` to start using the 
-:doc:`{+atlas-cli+} commands </command/atlas>`.
+:ref:`{+atlas-cli+} commands <atlas>`.
 
 .. toctree::
    :titlesonly:

source/migrate-to-atlas-cli.txt

@@ -20,7 +20,7 @@ Migrate to the {+atlas-cli+}
 
    ``mongocli atlas`` commands for MongoCLI are now deprecated. Follow
    the steps on this page to migrate to the {+atlas-cli+} and run
-   :doc:`{+atlas-cli+} commands </command/atlas>` instead of
+   :ref:`{+atlas-cli+} commands <atlas>` instead of
    ``mongocli atlas`` commands.
 
 If you have already configured {+mcli+}, you can migrate your settings to the
@@ -47,7 +47,7 @@ following steps to migrate from the {+mcli+} to the {+atlas-cli+}:
              If you use any automation scripts that rely on ``mongocli.toml`` or
              use {+mcli+} |service| commands, update the scripts to point to the
              :ref:`new configuration file <config-toml-location>` and use 
-             :doc:`{+atlas-cli+} commands </command/atlas>` instead.
+             :ref:`{+atlas-cli+} commands <atlas>` instead.
 
              .. note::
 
@@ -66,9 +66,9 @@ following steps to migrate from the {+mcli+} to the {+atlas-cli+}:
              You can authenticate using either ``atlas auth login`` or ``atlas
              config init``. To learn more, see :ref:`<connect-atlas-cli>`.
 
-   .. step:: Use the new :doc:`{+atlas-cli+} commands </command/atlas>`.
+   .. step:: Use the new :ref:`{+atlas-cli+} commands <atlas>`.
 
-             Use :doc:`{+atlas-cli+} commands </command/atlas>` (starting
+             Use :ref:`{+atlas-cli+} commands <atlas>` (starting
              with ``atlas``) wherever you previously used {+mcli+} |service|
              commands (starting with ``mongocli atlas``). You can use profiles
              that {+atlas-cli+} migrates