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Suzanne, we've looked into this and we've compared our overrides to the joomla ones and they are basically identical. We don't see anything that could be a security issue at all. BTW, in your paste above you have referenced gantry overrides that we use when running Joomla 3.0, that basically fall back to the same output as we use in our 2.5 templates (for compatibility). These files are not even used by your Joomla 2.5.18 install.
My hunch is that this security script that is reporting this is just scanning files and finding our overrides and doesn't really know what to do with them. I am confident this is not a security issue, but more of a false alarm type situation.
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The following users have thanked you: suzanne roelse