today, restarts had no effect, the problem occurred every time i tried to work with my workspace, i had to kill the ide several times.
a fresh install of my eclipse version (7.5, 3.4.2, M20090211-1700) seemed to help, i’ve opened my workspace and “initializing java tooling” finished without problems.
i’m calling eclipse with the -configuration switch, so no settings are lost (config path is some home subdirectory).
btw: the thread dump says, the problem occurs (in my case) because of a classloading deadlock (eclipse core), see https://www.genuitec.com/forums/topic/hint-identifying-problems/ for howto identify deadlocks with jvisualvm.
cheers,
g.