Some dependency version upgrades

Taking the opportunity to make a deps upgrade before the move to locationtech:

- ae8025d Upgrade logback from `1.0.13` to `1.1.12`
- 3c5a893 Upgrade JCommander from `1.30` to `1.35`
- bce4e42 Upgrade compress-lzf from `0.9.8` to `1.0.1`
- 2bb2660 Upgrade Berkeley DB Java Edition from `5.0.84` to `5.0.104`