I dont think its really smart to rename the index.php, cant you instead make your webserver rewrite the requests made to default.php, or make index.php one of the default "serving pages" ? I think its refered to several times in the ezpublish php code..
The "index.php" name is buried in the code and things can break if a different name is used. Specifically, to find the base URL for images a string search for "index.php" is done in some configurations. If that is needed and fails, the pages look quite ugly. I've reported several related issues.
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