Fix entries closing on saving compiled script to jar:

also adding a short sleep in tests, otherwise in some cases the
classloader was not able to find class in the jar.
Fixes script to jar saving tests on windows

libraries/scripting/jvm-host-test/test/kotlin/script/experimental/jvmhost/test/ScriptingHostTest.kt

@@ -112,6 +112,7 @@ class ScriptingHostTest : TestCase() {
         val compilationConfiguration = createJvmCompilationConfigurationFromTemplate<SimpleScriptTemplate>()
         val host = BasicJvmScriptingHost(evaluator = BasicJvmScriptJarGenerator(outJar))
         host.eval("println(\"$greeting\")".toScriptSource(name = "SavedScript.kts"), compilationConfiguration, null).throwOnFailure()
+        Thread.sleep(100)
         val classloader = URLClassLoader(arrayOf(outJar.toURI().toURL()), ScriptingHostTest::class.java.classLoader)
         val scriptClass = classloader.loadClass("SavedScript")
         val output = captureOut {
@@ -139,6 +140,8 @@ class ScriptingHostTest : TestCase() {
             saver(compiledScript, ScriptEvaluationConfiguration.Default).throwOnFailure()
         }
 
+        Thread.sleep(100)
+
         val classpathFromJar = run {
             val manifest = JarFile(outJar).manifest
             manifest.mainAttributes.getValue("Class-Path").split(" ") // TODO: quoted paths

libraries/scripting/jvm-host/src/kotlin/script/experimental/jvmhost/jvmScriptSaving.kt

@@ -70,19 +70,23 @@ fun KJvmCompiledScript<*>.saveToJar(outputJar: File) {
             putValue("Created-By", "JetBrains Kotlin")
             if (dependencies.isNotEmpty()) {
                 // TODO: implement options for various cases - paths as is (now), absolute paths (local execution only), names only (most likely as a hint only), fat jar
-                putValue("Class-Path", dependencies.joinToString(" "))
+                putValue("Class-Path", dependencies.joinToString(" ") { it.toURI().toURL().toExternalForm() })
             }
             putValue("Main-Class", scriptClassFQName)
         }
-        // TODO: fat jar/dependencies
-        val jarStream = JarOutputStream(fileStream, manifest)
-        jarStream.putNextEntry(JarEntry(scriptMetadataPath(scriptClassFQName)))
-        jarStream.write(copyWithoutModule().toBytes())
-        for ((path, bytes) in module.compilerOutputFiles) {
-            jarStream.putNextEntry(JarEntry(path))
-            jarStream.write(bytes)
+        JarOutputStream(fileStream, manifest).use { jarStream ->
+            jarStream.putNextEntry(JarEntry(scriptMetadataPath(scriptClassFQName)))
+            jarStream.write(copyWithoutModule().toBytes())
+            jarStream.closeEntry()
+            for ((path, bytes) in module.compilerOutputFiles) {
+                jarStream.putNextEntry(JarEntry(path))
+                jarStream.write(bytes)
+                jarStream.closeEntry()
+            }
+            jarStream.finish()
+            jarStream.flush()
         }
-        jarStream.finish()
+        fileStream.flush()
     }
 }