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DirectoryIndex index.php index.html
will cause index.php to be the first page loaded, if it's not there there then index.html will be loaded.
index.php has PR0 because you have been linking to the default page (probably index.html). Changing the DirectoryIndex will allow index.php to assume the PR of the default page.
your-domain.com/ = PR
your-domain.com/index.php = No PR
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