Transition CIME to using a custom util for copying files. #2475
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The file-copy operation is very common in CIME and we were using
a smattering of shutil.copyfile, shutil.copy, and shutil.copy2.
This PR replaces these with safe_copy, a flexble and fault-tolerant
copying function. This should make it much easier for users to share
case directories and other common directories.
Test suite: scripts_regression_tests
Test baseline:
Test namelist changes:
Test status: bit for bit
Fixes [CIME Github issue #]
User interface changes?: N
Update gh-pages html (Y/N)?: n
Code review: @jedwards4b