Yeah, it's a bit tricky.
If we choose the "Easy" One-Click method, we don't actually have access to any files. They're maintained by DreamHost on a different server so we never have to bother with updating core stuff.
With the "Advanced" method the files are stored in our own user-space on our server, and as such we have file-level access to everything (which is necessary if you want to install diferent themes, plug-ins, etc.)
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How To Install PHP.INI / ionCube on DreamHost