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"the fork" refers to ACME's fork of CIME:  https://github.com/ACME-Climate/cime

"the subtree" refers to all the code under https://github.com/ACME-Climate/ACME/cime

 

When modifications from within the subtree need be moved back to the fork:

From inside the ACME branch (or master) that contains the changes:

 

 

 

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