Remove a VM from the threads list when discarding it

Previously there were cases where we weren't properly removing the
thread from the threads list. This happened for example for the
SignalHandler thread and QueryAgent thread.

By always removing it from the threads list from VM::discard, we make
sure it's always remove and does not cause a crash when the GC tries to
scan a thread that was not running anymore.

vm/builtin/thread.cpp

@@ -228,8 +228,6 @@ namespace rubinius {
     vm->thread->cleanup();
     vm->thread->init_lock_.unlock();
 
-    vm->shared.remove_managed_thread(vm);
-
     // Clear the call_frame, so that if we wait for GC going independent,
     // the GC doesn't see pointers into now-unallocated CallFrames
     vm->set_call_frame(0);

vm/shared_state.cpp

@@ -125,6 +125,7 @@ namespace rubinius {
 
   void SharedState::remove_vm(VM* vm) {
     SYNC_TL;
+    threads_.remove(vm);
     this->deref();
 
     // Don't delete ourself here, it's too problematic.