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Can I safely rename the cygdrive folder? Also, I would like to add other folders at root and map them to folders on windows in the same way as /cygdrive/c maps to my C drive. Is that possible?

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Yes, you can. See The Cygwin Mount Table in Cygwin's documentation. I have my documents folder mounted as /doc. These mounts end up in the registry and are retained across reboots etc.

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I wouldn't rename cygdrive as I don't know what that would do, but you can map other directories at root to various windows directories using the mount command.

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