some people add directory to module classpath by making it a library instead of a source root, let the module scope accept that (http://devnet.jetbrains.net/message/5291160#5291160)

java/java-tests/testSrc/com/intellij/roots/ModuleScopesTest.java

@@ -201,4 +201,15 @@ public class ModuleScopesTest extends ModuleTestCase {
 
     return libraryRoot;
   }
+
+  public void testLibUnderModuleContent() throws IOException {
+    VirtualFile lib = myFixture.findOrCreateDir("lib");
+    ModifiableRootModel model = ModuleRootManager.getInstance(myModule).getModifiableModel();
+    model.addContentEntry(lib);
+    model.commit();
+
+    VirtualFile file = lib.createChildData(this, "a.txt");
+    addLibrary(myModule, DependencyScope.COMPILE);
+    assertTrue(myModule.getModuleWithDependenciesAndLibrariesScope(false).contains(file));
+  }
 }

platform/lang-impl/src/com/intellij/openapi/module/impl/scopes/ModuleWithDependenciesScope.java

@@ -118,7 +118,10 @@ public class ModuleWithDependenciesScope extends GlobalSearchScope {
 
   @Override
   public boolean contains(VirtualFile file) {
-    return myRoots.contains(getFileRoot(file));
+    if (myProjectFileIndex.isInContent(file) && myRoots.contains(myProjectFileIndex.getSourceRootForFile(file))) {
+      return true;
+    }
+    return myRoots.contains(myProjectFileIndex.getClassRootForFile(file));
   }
 
   @Override