Don't consider a directory to be a package if there's a .java or .class file with the same name in its parent directory

#KT-12664 Fixed

compiler/cli/src/org/jetbrains/kotlin/cli/jvm/index/JvmDependenciesIndexImpl.kt

@@ -220,7 +220,7 @@ class JvmDependenciesIndexImpl(_roots: List<JavaRoot>): JvmDependenciesIndex {
                 }
             }
             else {
-                currentFile = currentFile.findChild(subPackageName) ?: return null
+                currentFile = currentFile.findChildPackage(subPackageName, pathRoot.type) ?: return null
             }
 
             val correspondingCacheIndex = pathIndex + 1
@@ -233,6 +233,21 @@ class JvmDependenciesIndexImpl(_roots: List<JavaRoot>): JvmDependenciesIndex {
         return currentFile
     }
 
+    private fun VirtualFile.findChildPackage(subPackageName: String, rootType: JavaRoot.RootType): VirtualFile? {
+        val childDirectory = findChild(subPackageName) ?: return null
+
+        // Resolve conflicts between files and packages with the same qualified name in favor of files
+        val fileExtension = when (rootType) {
+            JavaRoot.RootType.BINARY -> ".class"
+            JavaRoot.RootType.SOURCE -> ".java"
+        }
+
+        if (findChild(subPackageName + fileExtension)?.isDirectory == false) {
+            return null
+        }
+        return childDirectory
+    }
+
     private fun cachesPath(path: List<String>): List<Cache> {
         val caches = ArrayList<Cache>(path.size + 1)
         caches.add(rootCache)