Add only non-jdk classpath entries from the compiler to script

remove unnecessary manifest classpath entries in the saved compiled
script jar

plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/ScriptJvmCompilerImpls.kt

@@ -11,6 +11,8 @@ import org.jetbrains.kotlin.cli.common.messages.MessageCollector
 import org.jetbrains.kotlin.cli.jvm.compiler.KotlinCoreEnvironment
 import org.jetbrains.kotlin.cli.jvm.compiler.NoScopeRecordCliBindingTrace
 import org.jetbrains.kotlin.cli.jvm.compiler.TopDownAnalyzerFacadeForJVM
+import org.jetbrains.kotlin.cli.jvm.config.JvmClasspathRoot
+import org.jetbrains.kotlin.cli.jvm.config.JvmContentRoot
 import org.jetbrains.kotlin.cli.jvm.config.jvmClasspathRoots
 import org.jetbrains.kotlin.codegen.ClassBuilderFactories
 import org.jetbrains.kotlin.codegen.KotlinCodegenFacade
@@ -126,7 +128,8 @@ private fun compileImpl(
                 // performed with the expected classpath
                 // TODO: make this logic obsolete by injecting classpath earlier in the pipeline
                 val depsFromConfiguration = get(dependencies)?.flatMapTo(HashSet()) { (it as? JvmDependency)?.classpath ?: emptyList() }
-                val depsFromCompiler = context.environment.configuration.jvmClasspathRoots
+                val depsFromCompiler = context.environment.configuration.getList(CLIConfigurationKeys.CONTENT_ROOTS)
+                    .mapNotNull { if (it is JvmClasspathRoot && !it.isSdkRoot) it.file else null }
                 if (!depsFromConfiguration.isNullOrEmpty()) {
                     val missingDeps = depsFromCompiler.filter { !depsFromConfiguration.contains(it) }
                     if (missingDeps.isNotEmpty()) {