Waiting lines can get clobbered by a directory sync

Since *waiting* lines don't count as making a file *running*, the main loop will happily initiate a directory sync which kills any reference to the waiting lines.  This is exacerbated by the fact that, while a file is running, the poll time decreases from 60 seconds to 10, which means that a rescan can happen in as little as 10 minutes.  

This means that if you have a line `A` and another line `B` that runs after it, and `A` takes 10 or more minutes, and nothing else happens to be running when `A` finishes, you're guaranteed that `B` won't run as expected.  Not only that, but there will be no logging anywhere that `B` didn't run.