regenerate certificates -- and use oracle in a few cases where the Z3 proof parser can't deal with Z3 3.2 proofs

Z3's soft timeout is expressed in ms, not in s -- this explains the frequenty "error code 112" failures we had recently

dropped relics of ancient side-entry points

prefer JDialog over JWindow to avoid focus inversion problem on Compiz (e.g. Ubuntu/Unity 12.10): both JDialog and JFrame happen to work, but JFrame does not support parent nesting;

tuned signature;

tuned imports;

include user counters as well;

scala mode is already part of jedit-5.0.0;

tuned;

simplified quick start via "isabelle components -I";