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Having a symlink:

ln -s /var/www /media/Disk2/dropbox/www

How can I remove a folder from the symlink located at /media/Disk2/dropbox/www/test without afecting the main folder?

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Are you saying you want to remove /media/Disk2/dropbox/www/test without removing /var/www/test? That's not possible, they are one and the same folder. – Rob Wouters Jan 30 '12 at 17:20
up vote 2 down vote accepted

You can't, a symlink is just a file containing a pointer to the other folder(subdirectory).

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