[FIXED JENKINS-4047] don't mess with file permissions

ahochsteger asks 'why do we mess with file permissions anyway?' and he's
right! I digged the history but couldn't find why we do it.

I think we should just set the permissions of the top-level directories,
but leave the other file permissions as-is.

In addition,

- I see no point in touching usr/bin usr/sbin.
  perhaps C&P mistake from some samples?

- Don't touch /var/lib/hudson if .for-jenkins is present,
  so that people using the hudson user can keep upgrading new
  versions of jenkins and run it as hudson

- /var/run/hudson contains no important information,
  so no need to bring it over to /var/run/jenkins