Gnome 3 extensions, theme, and default applications messed up

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https://bbs.archlinux.org – After freaking out yesterday when I restarted my computer after the last upgrade and being greeted with a nice gnome error screen, I have finally got my computer to work again. I made all the changes to move it towards initscripts and I am currently running in the systemd/initscripts mixed mode (however, my daemons array is empty except hwclock (not sure if I even need that anymore...) so I will be moving towards pure systemd soon). After managing to get GDM and Gnome (now 3.6.1) started again I was greeted by an unthemed, unextensioned, vanilla workspace as though it had just been installed.I (HowTos)