Add documentation around the cli

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diff --git a/docs/source/internal/cli.rst b/docs/source/internal/cli.rst
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+Command Line Interface
+======================
+
+The command line interface of Flake8 is modeled as an application via
+:class:`~flake8.main.cli.Application`. When a user runs ``flake8`` at their
+command line, :func:`~flake8.main.cli.main` is run which handles
+management of the application.
+
+User input is parsed *twice* to accomodate logging and verbosity options
+passed by the user as early as possible so as much logging can be produced as
+possible.
+
+The default flake8 options are registered by
+:func:`~flake8.main.cli.register_default_options`. Trying to register these
+options in plugins will result in errors.
+
+
+API Documentation
+-----------------
+
+.. autofunction:: flake8.main.cli.main
+
+.. autoclass:: flake8.main.cli.Application
+    :members:
+
+.. autofunction:: flake8.main.cli.register_default_options