From the conversation at commons:User_talk:Faidon_Liambotis_(WMF)#GWT_throttling it seems that the files downloaded by GWToolset are only deleted when the whole batch upload sequence is finished. Given that the files it uploads tend to be fairly large and one sequence can include thousands or even hundreds of thousands of them, and the files are published on Wikipedia as soon as they are downloaded (so they are not needed anymore once the upload job finishes), this might be suboptimal.

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