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Updates the clone folder so that it contains all the files in the original folder.
Two passes are made. First the clone folder is traversed to see if it's missing any files in the original. Any missing files are copied into the clone.
Any files or sub-folders that were modified more recently than the files in the clone are also copied.
In the second pass, the clone folder is traversed to see if it contains any files or sub-folders that don't exist in the original. Those files are moved to the "Extra Files" sub-folder in the clone, which is created if it doesn't already exist.
The copyFilter callback routine is passed to file.filteredCopy, allowing you to override any copying, or to create a report of any files that were copied. See the docs for file.filteredCopy for details.
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