I know if I use the GUI, I can load all folders in Filter/Archives then Extract All to the directory of my choosing. But this won't delete the archives (or more importantly, their parent folders), so I will have to load these in the Rename section of the GUI as well. Filebot seems to want to rename the .r01, .r02, .r03 files in addition to the, say, .mkv file for the movie.
If I wanted to use the CLI first, I could use
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filebot -extract -r "Movies/to/Process" --output "Directory/of/my/choosing"
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--def deleteAfterExtract=y
There might be a way to use 7-zip for the extraction portion instead. Something like is shown here:
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https://superuser.com/questions/371384/extract-all-zips-in-a-directory-incl-subfolders-with-a-bat-file-or-dos-comm