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How would I get WUBI to install to a specified directory other than the default one in c drive? In Windows 7. Could I get all of the files to maybe go to the hidden boot folder also on the C: drive.

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By default wubi installer shows only the disk drive letters only during the installation. After the installation you may make that Ubuntu folder as a hidden folder by right click and set properties. If you hide or move the installation folder to some other location you have to edit the GRUB menu manually by mentioning the new location .It will more risky for normal users.

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