Started controller and installed netconf connector and BGP features. Left controller running for a few min then tried to stop. It didnt stop. Left it in this state over-night. The process was still up next day.

Analysis of thread dumps reveals that DOMForwardedWriteTransaction.cancel() never returns.
The faulty code seems to be

do {
future = commitFuture;
} while (future == null);

Future is always null, hence this call never returns.

Thread dumps and logs are attached.