CESM2.1 release branch updates

CESM2.0 release branch updates

CESM2.0.0 Release

CESM2.0.0 Release

Release candidate for cesm2.0.0

Last beta tag before cesm2.0.0 release.

This will contain the release tags for each component and will comprise what we release as cesm2.0.0

More changes for the code freeze

CLM answer changes, final POP, final model_doi_url changes

CAM answer changes. Update components for model_doi_url

Tagging cesm2_0_alpha10d

Rework git logic for determining in-sync and current ref name

Rework two aspects of the logic for git repositories; both of these can
change behavior in some cases when printing status:

1. Determining whether the local checkout is in-sync with the expected
   reference from the configuration file: Now we always convert the
   expected reference to a hash and compare that with the
   currently-checked-out hash. Previously, we sometimes did the
   comparison using names, e.g., just ensuring that you're on the right
   branch.

2. Determining the current ref name (e.g., the branch or tag currently
   checked out). Now we use a number of plumbing commands rather than
   relying on regex parsing of 'git branch -vv'. The previous regex
   parsing was fragile and hard to maintain, and was the source of a
   number of bugs. In addition, differences between git v. 1 and git
   v. 2 meant that the result was incorrect in some cases -
   particularly, in the case where we have "detached from foo" (which is
   the text that always appeared for a detached head in v 1, but in v 2
   means we are no longer at foo).

This results in some subtle changes to status output. One particular
change is: If we're on a tracking branch, `checkout_externals -S -v`
will show the name of the local branch rather than the tracked
branch. (This is more accurate, because we may not actually be at the
head of the tracking branch.)

Also some other minor changes to documentation and running code coverage.

Tagging cesm2_0_alpha10c

Feature release 1.1.0 for manage_externals

* Add schema support for explicitly specifying a git hash. This schema change is
backwards compatible with older input files, but adds new functionality that
can not be used with prior versions of manage_externals.

Bugfix tag 1.0.2 for manage_externals

Includes bugfixes for:

* svn and git authentication requests may not be displayed to the user on
  some machines. Add a timeout limit to subprocess calls.

* explicit configuration file schema version checking.

* Update readme and help, including working with local repositories, comments
  in externals files, switching repository types not supported.