Your packages are still wrong (should be data.scripts not just scripts). It works fine on my side just from changing data/scripts/SCModPlugin.java without touching the .jar, which still isn't being used.
Also don't duplicate Java files between the mod's data/scripts folder and what goes into the jar, at best it's confusing.
Also: why are you using command line instead an IDE? You're not even actually compiling the Java files as far as I can tell, just archiving them in a jar (as if it were a zip file).
What's he difference between ModPlugin and BaseModPlugin?
ModPlugin is an
interface, BaseModPlugin is a class implementing that interface.
But the only thing you need to know: you should
extend BaseModPlugin (that's what it's there for) instead of going to the trouble of implementing ModPlugin directly.
Also, when compiling, do I need to somehow link to the sarfarer.api?
Yes. (The fact that it hasn't already thrown a compile error is further evidence that it's not actually being compiled. Seriously, get an IDE, it'll save heaps of effort in the medium and long term.)