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Same here, Win 7 x64. Ctrl+Space opens up the list of all actions, so you can make your way from there.

A bit of an annoyance, but apparently being able to evaluate and update multiple files in a Clojure project works now, so I'm too happy to care.

>it's fixed in master. Will go out tonight.

I have the same issue... not sure how to get them back either. I'm on windows 7 x64.

Do they come up if you press the Alt key?

Win 7 x64. No menus. Alt key does nothing.