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)

compiler/testData/compileKotlinAgainstCustomBinaries/innerClassPackageConflict/library/test/Foo.java

@@ -0,0 +1,7 @@
+package test;
+
+public class Foo {
+    public interface Bar {
+
+    }
+}

compiler/testData/compileKotlinAgainstCustomBinaries/innerClassPackageConflict/output.txt

@@ -0,0 +1 @@
+OK

compiler/testData/compileKotlinAgainstCustomBinaries/innerClassPackageConflict/source.kt

@@ -0,0 +1,3 @@
+import test.Foo.Bar
+
+val f: Bar? = null

compiler/tests-common/org/jetbrains/kotlin/test/MockLibraryUtil.java

@@ -155,7 +155,7 @@ public class MockLibraryUtil {
         }
     }
 
-    private static File createJarFile(File contentDir, File dirToAdd, String sourcesPath, String jarName, boolean addSources) throws IOException {
+    public static File createJarFile(File contentDir, File dirToAdd, String sourcesPath, String jarName, boolean addSources) throws IOException {
         File jarFile = new File(contentDir, jarName + ".jar");
 
         ZipOutputStream zip = new ZipOutputStream(new FileOutputStream(jarFile));

compiler/tests/org/jetbrains/kotlin/jvm/compiler/CompileKotlinAgainstCustomBinariesTest.java

@@ -40,10 +40,7 @@ import org.jetbrains.kotlin.load.kotlin.JvmMetadataVersion;
 import org.jetbrains.kotlin.resolve.BindingContext;
 import org.jetbrains.kotlin.resolve.DescriptorUtils;
 import org.jetbrains.kotlin.resolve.lazy.JvmResolveUtil;
-import org.jetbrains.kotlin.test.ConfigurationKind;
+import org.jetbrains.kotlin.test.*;
-import org.jetbrains.kotlin.test.KotlinTestUtils;
-import org.jetbrains.kotlin.test.TestCaseWithTmpdir;
-import org.jetbrains.kotlin.test.TestJdkKind;
 import org.jetbrains.kotlin.test.util.DescriptorValidator;
 import org.jetbrains.kotlin.test.util.RecursiveDescriptorComparator;
 import org.jetbrains.kotlin.utils.ExceptionUtilsKt;
@@ -440,4 +437,14 @@ public class CompileKotlinAgainstCustomBinariesTest extends TestCaseWithTmpdir {
                 new File(getTestDataDirectory(), "output.txt"), normalizeOutput(outputMain)
         );
     }
+
+    public void testInnerClassPackageConflict() throws Exception {
+        compileJava("library");
+        FileUtil.copy(new File(getTestDataDirectory(), "library/test/Foo/x.txt"),
+                      new File(tmpdir, "library/test/Foo/x.txt"));
+        MockLibraryUtil.createJarFile(tmpdir, new File(tmpdir, "library"), null, "library", false);
+        File jarPath = new File(tmpdir, "library.jar");
+        Pair<String, ExitCode> output = compileKotlin("source.kt", tmpdir, jarPath);
+        KotlinTestUtils.assertEqualsToFile(new File(getTestDataDirectory(), "output.txt"), normalizeOutput(output));
+    }
 }