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I have been forced – by the wp plugin police – to improve security on import proc to avaoid hackers to misuse it.
Even today a few extra checks will be included to assure decent use of authorized users only.
For this reason you may no longer include folders in a zip.
You can still ftp a folder structure with content to your depot that will be imported according to its stucture.
Sorry for the inconvenience, but it is better for us all.