While this YouTrack issue is related to fat JARs, this also can happen if you aren't using fat JARs (loading all the libraries via the startup classpath option or the Class-Path manifest option)
To fix this, or you can all your dependencies on your startup script like this:
-Dkotlin.script.classpath=jar1:jar2:jar3:jar4
Example:
java -Dkotlin.script.classpath=libs/dependency1.jar:libs/dependency2.jar:yourjar.jar -jar yourjar.jar
Or, if you prefer, set the property via code, using your Class-Path manifest option.
val path = this::class.java.protectionDomain.codeSource.location.path
val jar = JarFile(path)
val mf = jar.manifest
val mattr = mf.mainAttributes
// Yes, you SHOULD USE Attributes.Name.CLASS_PATH! Don't try using "Class-Path", it won't work!
val manifestClassPath = mattr[Attributes.Name.CLASS_PATH] as String
// The format within the Class-Path attribute is different than the one expected by the property, so let's fix it!
// By the way, don't forget to append your original JAR at the end of the string!
val propClassPath = manifestClassPath.replace(" ", ":") + ":Loritta-0.0.1-SNAPSHOT.jar"
// Now we set it to our own classpath
System.setProperty("kotlin.script.classpath", propClassPath)
While I didn't test this yet, in another unrelated answer it seems you can also supply your own classpath if you initialize the KotlinJsr223JvmLocalScriptEngine object yourself (as seen here)