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Migrating my site from Ubuntu 9.04 to RedHat 5 - directory issues

Hi All,
I'm attempting to migrate my website files from server Ubuntu 9.04 to RedHat 5. it's currently hosted in directory

but in RedHat 5 the root directory is

I just want to know if avoioding/ignoring the document directory and placing my intranet folder in the same www directory will cause problems.
Any assistance appreciated!
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