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I know :) I'm an idiot :)

I did chmod -R 777 /usr

I was able to run chmod -R 755/usr from recovery mode. Now almost all work well. But the Software update and a few other futures still don't work.

Anybody knows default permissions for the content of /usr?

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Well you used the -R (recursive) flag then your system is screwed , the best solution is to reinstall Ubuntu.

Another way to fix it, is to install the same version of Linux on another machine (or VM) then just copy /usr over to the old machine , good luck.

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