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Update readme and help output

Update the readme and help output for checkout_externals to:

* clarify basic operation as explicit and data driver

* remove some cesm specific names in examples

* Document format externals description file and comments.

* Note that switching repositiory protocol is not supported. Must manually move
  the old repository.

* Document a work-around to avoid safety checks on modified files.

* Document that using the 'externals_only' protocol on the top level repository
  requires specifying the local_path as '.'

Testing:
  make test - python2 - all tests pass

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