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--preserve-structure: keep the source directory layout inside the destination instead of flattening.
Notes
By default the destination is computed from the raw source input as <source> ReOrganised adjacent to the original folder (so it won't create a C:\... folder inside your Linux home).
If you prefer skipping duplicate files instead of renaming, or want a --dry-run flag to preview actions, open an issue or request the change.
Example
Flatten a Desktop folder into a single collection (WSL or Windows):