This could be an odd permissions issue, but running ls -l seems to be fine. I installed multiple extensions manually to /usr/share/gnome-shell/extensions by moving them from my local extensions directory. However, these extensions no longer show up in Gnome Tweak Tool and are no longer applied.
Here is the output of ls -l /usr/share/gnome-shell/extensions
total 80
drwxr-xr-x 2 root root 4096 Apr 11 23:10 alternate-tab@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 apps-menu@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 auto-move-windows@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 5 root root 4096 Aug 8 20:28 caffeine@patapon.info
drwxr-xr-x 5 root root 4096 Aug 8 20:28 dash-to-panel@jderose9.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 drive-menu@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 4 root root 4096 Aug 8 20:28 dynamicTopBar@gnomeshell.feildel.fr
drwxr-xr-x 3 root root 4096 Aug 8 20:28 impatience@gfxmonk.net
drwxr-xr-x 2 root root 4096 Apr 11 23:10 launch-new-instance@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 native-window-placement@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 places-menu@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Aug 8 20:28 refresh-wifi@kgshank.net
drwxr-xr-x 2 root root 4096 Aug 8 20:28 remove-dropdown-arrows@mpdeimos.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 screenshot-window-sizer@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 4 root root 4096 Aug 8 20:28 suspend-button@laserb
drwxr-xr-x 3 root root 4096 Aug 8 20:28 TopIcons@phocean.net
drwxr-xr-x 2 root root 4096 Apr 11 23:10 user-theme@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 window-list@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 windowsNavigator@gnome-shell-extensions.gcampax.github.com
drwxr-xr-x 2 root root 4096 Apr 11 23:10 workspace-indicator@gnome-shell-extensions.gcampax.github.com
The extensions from gnome-shell-extensions.gcampax.github.com came installed with Ubuntu Gnome and are working normally. However, all of the other extensions do not show up in Tweak Tool at all. Any ideas?