Duplicate photos from root Picture folder

As a result of upgrading versions of LR from 1.0 to now, and not knowing how to do that properly, I've got nested Lightroom and Pictures sub folders in my root Pictures on my Mac system.  Is there a way to illiminate duplicate photos, without breaking the LR catalog?  There are no duplicates in my catalog.

I have LR pointing, on my iMac, to the "Pictures" folder.  Under that, I have sub folders called "Lightroom->Pictures", etc.  I have many more pictures and folders under root->Pictures, than I have in my LR catalog.  I think upgrading since 1.0 has duplicated on import and created new folders.  I want to clean this up now and delete duplicate raw images on disk.  I can't do it manually.  Too onerous. Hope that makes this simple situation clearer.
Update: Turns out i only have 2k extra images than what appears in the catalog, so maybe not as bad as I thought.  Would still like to reorganize the folders so that they make more sense, like illiminating the lightroom->pictures sub-folders.
Update: Found the easiest way to reorganize is to global highlight photos in a sub folder and drag to the higher level folder.  LR does all the work and updates the catalog.  Solved.

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