StopMongoProgram (which powers the shell's MongoRunner.stopMongod) will switch to SIGKILL after waiting a while, then still reports successful shutdown. This both masks bugs that deadlock at shutdown and can cause problems for tests that actually need to wait for full clean shutdown. The only indication that this happens is a line in the log, but no one will read that if the test is passing.
Instead, the shell will now wait forever for a mongod program to terminate via a SIGTERM. If a process indeed is deadlocked at shutdown, resmoke will now run the hang analyzer on the stuck process.