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Zip files can already be copied into or used as a base folder in the current version of BC3 (3.3.3). You can setup a Folder Sync session and sync to a target (zip) using the graphical interface.
Beyond Compare is a multi-platform utility that combines directory compare and file compare functions in one package. Use it to manage source code, keep directories in sync, compare program output, etc.
Are you looking for different or additional behavior?
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