We've had people report this but we've been unable to reproduce it ourselves.
Could you please share your hardware specs, and your java specs (version, vendor, etc.)?
Edit: Also, can you reproduce this issue on the standalone launcher without Twitch?
It's as if a clean shutdown is the INTENDED way for the server to shutdown!
If you kill the server process WHILE the server is saving you are likely to corrupt the world.
Also shouldn't you be using screen for things like this?
You would be best off writing them from scratch.
Know that if you endeavor to do so you will find no help here. Around here we move forwards, not backwards.
CurseForge is the recommended site for mods.
As for that error, you shouldn't need a JDK, a JRE should do.
I'd recommend getting a Java 8 JRE from here, click here for a direct download of the MacOS version.