PY-44858 Create regular packages in refactorings initiated from top-level files in source/content roots

Otherwise, if someone wants to move a definition/extract a superclass from there to
a brand-new package, e.g. from main.py to pkg/mod.py, a namespace "pkg" package will
be created.

Restore the original behavior of PyExtractSuperclassTest.testMultifileNew: the origin
file was inside a regular project root without __init__.py alongside.

GitOrigin-RevId: 750414b18582740076c14bfcfd07fa38992b4428

python/python-psi-impl/src/com/jetbrains/python/psi/resolve/PyNamespacePackageUtil.kt

@@ -41,6 +41,7 @@ fun isNamespacePackage(element: PsiElement): Boolean {
 fun isInNamespacePackage(element: PsiElement): Boolean {
   val myFile = element.containingFile ?: return false
   val parentDirectory = myFile.containingDirectory
+  if (parentDirectory.virtualFile in PyUtil.getSourceRoots(element)) return false
   return parentDirectory != null && isNamespacePackage(parentDirectory)
 }
 

python/testData/refactoring/move/moveSymbolFromTopLevelModuleToNewPackageCreatesInitPy/after/src/pkg/subpkg/b.py

@@ -0,0 +1,2 @@
+class MyClass:
+    pass

python/testData/refactoring/move/moveSymbolFromTopLevelModuleToNewPackageCreatesInitPy/before/src/main.py

@@ -0,0 +1,2 @@
+class MyClass:
+    pass

python/testSrc/com/jetbrains/python/refactoring/PyMoveTest.java

@@ -427,6 +427,12 @@ public class PyMoveTest extends PyTestCase {
     });
   }
 
+  public void testMoveSymbolFromTopLevelModuleToNewPackageCreatesInitPy() {
+    doComparingDirectories(testDir -> {
+      moveSymbols(testDir, "pkg/subpkg/b.py", "MyClass");
+    });
+  }
+
   //PY-44858
   public void testMoveNotCreateInitPyForNamespacePackagesToAnotherDirectory() {
     doMoveSymbolsTest("pkg/subpkg/B/module_b.py", "myfunc");