Rewrite scripting related API to PsiFile instead of VirtualFile

There were several places where we converted virtualFile to PsiFile. This operation need a read access and may throw ProcessCanceledException,
so we want to minimize its usages in IDE

idea/idea-jvm/src/org/jetbrains/kotlin/idea/scratch/compile/KtScratchExecutionSession.kt

@@ -166,7 +166,7 @@ class KtScratchExecutionSession(
         }
 
         ScriptDependenciesManager.getInstance(originalFile.project)
-            .getRefinedCompilationConfiguration(originalFile.virtualFile)?.valueOrNull()?.let {
+            .getRefinedCompilationConfiguration(originalFile)?.valueOrNull()?.let {
                 javaParameters.classPath.addAll(it.dependenciesClassPath.map { f -> f.absolutePath })
             }