Today my SFTP plugin stopped working, additionaly context menu on the file list also stopped functioning

Try checking the console errors and creating issues for each plugin (many are hosted on github). Additionally, you may want to see if there is a “debug” setting in some form to provide more information for the issue you create.

I’ve got the same issue in Sublime Text 2 with the side bar, which it doesn’t show anything anymore, just a black area.
Disabling the option "theme": "Cobalt2.sublime-theme" in my user settings fixed the situation, although everything was fine until yesterday.
My colleagues have the same issue and I disabled their theme settings, but it’s not a problem of the single themes as we all use different ones.
Looking at the console I got this message: