El Capitan 10.11 Beta (15A263e), Safari Version 9.0 (11601.1.50)...
Nuked all my Extensions. Also changed permissions of my ~/Library/Safari/Extensions folder to be owned by root/wheel and rw-------.
The extensions were still there, but to get them back I had to move them out, create a new Extensions folder (maybe not necessary, I could have fixed permissions) and then reinstall the extensions one at a time.
At least it seems to be working now. But the contextual menu in Safari looks different, although without a before/after I can't say exactly how... But previously 1Password was always very close to the bottom, and now it is first in the section for Extension items.
