Most threads are marked as non-daemon

This basically means chunky will always require a `System.exit` to close, which can skip non-`finally` block resource closures.

This includes `Region Parser` and `3D Render Worker` threads, and a few others.

Start by locating the thread creation and shutdown paths for the Region Parser, 3D Render Worker, and other worker threads. Check how their daemon status affects application exit and resource cleanup, then verify that closing Chunky no longer requires System.exit and that resources still close through their normal lifecycle.

Written by the indexing model from the issue text.