clm4_5_18_r273: Support a standalone checkout from git

This PR allows a standalone git-based checkout to work. Starting with
this tag, we'll be using git rather than svn for CLM/CTSM development.

The biggest changes here are pulling in manage_externals, which serves
the role of svn externals. After cloning the repository, you can get all
of the necessary externals by running:

./manage_externals/checkout_externals

See the file README_EXTERNALS.rst at the top level of the repository for
more details on using this tool.

Other than that, this PR mostly involves changes to allow you to run
from the new directory structure of a standalone checkout: Now all of
the CLM/CTSM directories appear at the top level of the checkout, rather
than nested under components/clm.