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I used WineBottler to install Beyond Compare on my Mac. It runs within an X11 environment. (It works great, by the way.)

But it cannot access many folders to which my user account does not have permission, e.g, in the /System folder.

How can I run BC with "sudo" permissions?

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I haven't used WineBottler, but I'm assuming it creates an icon for the app in your Applications folder.

To run any App in OS X as sudo, open Terminal and enter the following:

sudo open -n $foo

Then drag the icon for the App from Finder into Terminal (replacing $foo in the example above). Press Enter and type your password. Voilà! Terminal launches the App as root.

Note that open -n works in Terminal to launch any $ as if it were launched via the Finder. (Otherwise it's impossible to launch and OS X app via Terminal as Apps are really just specialized directories on the filesystem-level.)

We trust you have received the usual lecture from the local System Administrator. It usually boils down to these three things:

#1) Respect the privacy of others.
#2) Think before you type.
#3) With great power comes great responsibility.

( I couldn't resist :P )

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This certainly works. I wish I could tick the accepted answer, but we'll need the OP to do that if they are so inclined. – bmike Jan 6 '14 at 21:12

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