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Here is an example of how you would set up the rewrite for a sub-directory installation. Notice that the RewriteRule specifies the subdirectories at the start, and redirects to that subdirectory in the rewrite. These subdirectories are also included in the rewrite exception for the webtop. If you have other exceptions you will need to update those as well.
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##### APACHE VERSION
RewriteEngine On
RewriteCond %{REQUEST_URI} !(/farcry|((subdirectory1|subdirectory2)/webtop|/flex2gateway|/flashservices)($|/)
RewriteRule ^/(subdirectory1|subdirectory2)([a-zA-Z0-9\/\-\%:\[\]\{\}\|\;\<\>\?\,\*\!\@\#\$\ \(\)\^_`~]*)$ /$1/index.cfm?furl=$2 [L,PT,QSA]
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