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However, I would like to limit this redirection to files that are in my root directory and exclude subdirectories from the redirect rule.
It would be fine to exclude all subdirectories or just exclude specific ones; I don't care.
Is there a way to do this?
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Redirect any URL which contains a slash followed by any number of characters which are not a slash, followed by ".html" to a resource of the same name in root, but without a file extension:
RedirectMatch permanent ^/([^/]*)\.html$ http://mysite.com/$1