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Wine directory structure used in Fedora Linux:
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${HOME}/.wine/drive_c is the root directory (aka C: drive) wine looks for it 
by default. It is created with (empty) C:\windows and C:\windows\system
directories, needed to operate Wine without an existing Windows
installation, if it does not already exist.

If you want to use Wine with an existing Windows installation that is
mounted, for example, in /mnt/windows-c, change the symlink
${HOME}/.wine/dosdevices/c: to point to /mnt/windows-c instead of the
defaults set by installation.

If you do this, you can safely remove ${HOME}/.wine/drive_c.
(Alternatively, just mount your Windows partition to ${HOME}/.wine/drive_c.)

Wine bugs:
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If you find a bug, please take the time to move your ${HOME}/.wine directory
someplace and try with a fresh version (like mv ${HOME}/.wine{,-save}). If the
bug is still there look trough https://bugzilla.redhat.com and see if the bug
is already reported. In case it is not please report it.