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The Generic Purge and Archive solution is designed to purge a directory with its sub directories or archive its content for future use.
The workflow consists of two separate sub processes implementing each of these functions. 

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Preserve Folder Structure in ARCHIVE Mode

Currently, this option is used as a part of zip command line options, so directory structure is not preserved and only files (without path) are stored in the archive. So if there are two or more files with the same name and extension (located in different folders) zipped using this option, then an error message will be generated and the rule will halt.

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-j

-junk-paths

Store just the name of a saved file (junk the path), and do not store directory names. By default, zip will store the full path (relative to the current directory). 

To preserve folder structure in ARCHIVE mode you should remove the -j option for the zip from the archive parameters.