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WAD Manager version 1.1 now contains USB support, and homebrew developer Waninkoko says that homebrew users on the Nintendo Wii will be able to manage their Virtual Console and WiiWare game data files on an attached USB drive.
Now we're not sure if the support is limited to USB flash or you could attach a USB external hard drive storage, but we can confirm that it works on Flash drives.
Waninkoko also advises that WAD Manager will not be able to read data from an attached USB drive as soon as the user inserts another SD card into the Wii console. It'll just spew corrupted data error messages.
To sort, install and store files on a USB drive, make sure that you follow the same procedure as you would for SD cards: create a folder named WAD in the root directory on the USB drive. File all your WAD collections there (from Virtual Console and WiiWare, we must add), and they should be accessible immediately after running WAD Manager v1.1.