After updating to the latest RC my site is loading the pages in the sites directory instead of the pages directory. I'm assuming when it updated it change the zone, but I'm not quite sure how that happened or why. I'm assuming I should probably make changes in the redirection manager, or would it just be easier to leave it be and upload my files from my pages directory over to the sites directory?

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Well hell! Now that is just totally strange. Never mind guys. I tried everything I could think of and it didn't make a difference, including clearing my browser cache and restarting my browser. However, I walked away for a few minutes and came back and refreshed my screen and it is all back to normal now. Now that is a Twilight Zone moment right there I'm telling ya

Hmm, maybe someone was playing with safe mode at some point? keep_safe_mode=1 would be in the URL if safe mode was on, and safe mode can only activate if you're logged in as an admin.

That could've been very possible. For all I know I may have even clicked on it while in the upgrader.php file. You know us blind guys … never watching what we're doing…