Thread calls for stop(), and start() are deprecated because they can cause deadlock situations when threads are vying for resources.
The primary use of threads in JLog is so that proof engine works independently from the interface. The only time these calls are made is when the user wishes to pause or halt a query. Since there are no inter-thread contentions we are likely safe.
It would be nice to retain the original functionality (pause, continue, abort) for queries, without producing a warning during compile.