Add section on AMReX Submodule

``[amrex options]`` is a list of any of the AMReX configuration options listed in the `AMReX user guide <https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html#building-with-cmake>`_

Working with the AMReX submodule

--------------------------------

For MFiX-Exa development or testing, you may need to build with a different

branch or release of AMReX.

The ``subprojects/amrex`` directory is a Git repo, so use all standard Git

commands. Either ``cd subprojects/amrex`` to run Git commands in the ``amrex``

directory, or use ``git -C subprojects/amrex`` in the MFiX-Exa repo. For

instance, to build with the ``my-amrex-branch`` branch of the AMReX repo:

.. code:: shell

    > git -C subprojects/amrex checkout my-amrex-branch

    > git status

    ...

    modified:   subprojects/amrex (new commits)

The branch ``my-amrex-branch`` will then be used when building MFiX-Exa.

To revert to the default version of the AMReX submodule, run ``git submodule

update``:

.. code:: shell

    > git submodule update

    > git status

    ...

    nothing to commit, working tree clean

You can edit, commit, pull, and push AMReX changes from ``subprojects/amrex``.

AMReX development is outside the scope of this document. Run ``git status`` in

the top-level MFix-Exa repo to see whether the AMReX submodule has new commits,

modified files, or untracked files.

To update the AMReX submodule reference by MFiX-Exa:

.. code:: shell

    > git add subprojects/amrex

    > git commit -m 'Updating AMReX version'

This will only update the AMReX SHA-1 referenced by MFiX-Exa. Uncommitted AMReX

changes and untracked AMReX files under ``subprojects/amrex`` are not added by

``git add subprojects/amrex``. Change directories to ``subprojects/amrex`` and

commit any AMReX changes first before ``git add subprojects/amrex``.

.. note::

    Only update the AMReX submodule reference in coordination with the other

    MFiX-Exa developers!

Few more notes on building MFiX-Exa

-----------------------------------