Recognize and override stale lock file
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The app sometimes seems to leave behind the lock file after a system shutdown and then, on the next start it will complain about the db being used by another instance. Looking at the lock file shows that it does record the PID (along with the username and the host name), so it would be pretty trivial to actually use that info and check if the process recorded in the lock file exists and if not, then just ignore and override the lock. (I'm not sure, BTW, while the lock file is needed at all, because the db file could be locked for writing through the OS, but that's a different question.)
Yes, his problem sometimes surfaces. However, in a situation where files are shared between computers, the check is far from trivial. The best detector is the user him/herself. If the lock file is stale, he/she can just throw it away. It might be good to mention this somewhere in the help file.