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When I try to access a Gopher site in Safari it opens OmniWeb to open the site. Where does Mac OS X or Safari store which application to use for Gopher sites? (I assume Safari doesn't support Gopher itself?)

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I'm guessing Safari uses Launch Services, which means it uses the system's default handler for that URL. These settings are stored in the file $HOME/Library/Preferences/com.apple.LaunchServices.plist. You can edit this using the defaults command in Terminal, or using a plain text editor if it is in the XML format.

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