diff --git a/jedi/api/refactoring.py b/jedi/api/refactoring.py
index 5bc3af58..9fbde02f 100644
--- a/jedi/api/refactoring.py
+++ b/jedi/api/refactoring.py
@@ -1,3 +1,5 @@
+from os.path import dirname, basename, join
+import re
 import difflib
 
 from parso import split_lines
@@ -54,36 +56,44 @@ class Refactoring(object):
 
         Returns ``Iterable[Tuple[str, str]]``.
         """
-        return self._renames
+        return sorted(self._renames)
 
     def get_diff(self):
-        return ''.join(f.get_diff() for f in self.get_changed_files())
+        text = ''
+        for from_, to in self.get_renames():
+            text += 'rename from %s\nrename to %s\n' % (from_, to)
+
+        return text + ''.join(f.get_diff() for f in self.get_changed_files())
 
     def apply(self):
-        for old, new in self._renames:
+        for old, new in self.get_renames():
             rename(old, new)
 
         for f in self.get_changed_files():
             f.apply()
 
 
-def _rename_path(path, new_name):
-    pass
+def _calculate_rename(path, new_name):
+    name = basename(path)
+    dir_ = dirname(path)
+    if name in ('__init__.py', '__init__.pyi'):
+        parent_dir = dirname(dir_)
+        return dir_, join(parent_dir, new_name, name)
+    ending = re.search(r'\.pyi?$', name).group(0)
+    return path, join(dir_, new_name + ending)
 
 
 def rename(grammar, definitions, new_name):
-    file_renames = []
+    file_renames = set()
     file_tree_name_map = {}
 
     for d in definitions:
-        if d.type == 'module':
-            file_renames.append(
-                (d.module_path, _rename_path(d.module_path, new_name))
-            )
+        tree_name = d._name.tree_name
+        if d.type == 'module' and tree_name is None:
+            file_renames.add(_calculate_rename(d.module_path, new_name))
         else:
             # This private access is ok in a way. It's not public to
             # protect Jedi users from seeing it.
-            tree_name = d._name.tree_name
             if tree_name is not None:
                 fmap = file_tree_name_map.setdefault(d.module_path, {})
                 fmap[tree_name] = tree_name.prefix + new_name
diff --git a/test/refactor.py b/test/refactor.py
index 3c263911..555f2071 100644
--- a/test/refactor.py
+++ b/test/refactor.py
@@ -32,7 +32,7 @@ class RefactoringCase(object):
         return f_name.replace('.py', '')
 
     def calculate_diff(self):
-        project = jedi.Project(os.path.join(test_dir, 'completion'))
+        project = jedi.Project(os.path.join(test_dir, 'refactor'))
         script = jedi.Script(self._code, path=self._path, project=project)
         refactor_func = getattr(script, self.refactor_type)
         refactor_object = refactor_func(self._line_nr, self._index, *self._args)
diff --git a/test/refactor/import_tree/mod.py b/test/refactor/import_tree/mod.py
new file mode 100644
index 00000000..ccb0f5e6
--- /dev/null
+++ b/test/refactor/import_tree/mod.py
@@ -0,0 +1 @@
+foobar = 3
diff --git a/test/refactor/rename.py b/test/refactor/rename.py
index b1ddd22c..db3f7fe9 100644
--- a/test/refactor/rename.py
+++ b/test/refactor/rename.py
@@ -43,44 +43,35 @@ def y():
      some_var = 3
      some_var
 # ----- import
-from import_tree.mod1 import foobarbaz
+from import_tree.mod import foobar
 #? 0 renamed
-foobarbaz
+foobar
 # +++++
---- /home/dave/source/jedi/test/completion/import_tree/mod1.py
-+++ /home/dave/source/jedi/test/completion/import_tree/mod1.py
-@@ -1,5 +1,5 @@
- a = 1
- from import_tree.random import a as c
- 
--foobarbaz = 3.0
-+renamed = 3.0
+--- /home/dave/source/jedi/test/refactor/import_tree/mod.py
++++ /home/dave/source/jedi/test/refactor/import_tree/mod.py
+@@ -1,2 +1,2 @@
+-foobar = 3
++renamed = 3
 --- /home/dave/source/jedi/test/refactor/rename.py
 +++ /home/dave/source/jedi/test/refactor/rename.py
 @@ -1,4 +1,4 @@
--from import_tree.mod1 import foobarbaz
-+from import_tree.mod1 import renamed
+-from import_tree.mod import foobar
++from import_tree.mod import renamed
  #? 0 renamed
--foobarbaz
+-foobar
 +renamed
 # ----- module
-from import_tree import mod1
+from import_tree import mod
 #? 0 renamedm
-mod1
+mod
 # +++++
---- /home/dave/source/jedi/test/completion/import_tree/mod1.py
-+++ /home/dave/source/jedi/test/completion/import_tree/renamedm.py
-@@ -1,5 +1,5 @@
- a = 1
- from import_tree.random import a as c
- 
--foobarbaz = 3.0
-+renamed = 3.0
+rename from /home/dave/source/jedi/test/refactor/import_tree/mod.py
+rename to /home/dave/source/jedi/test/refactor/import_tree/renamedm.py
 --- /home/dave/source/jedi/test/refactor/rename.py
 +++ /home/dave/source/jedi/test/refactor/rename.py
 @@ -1,4 +1,4 @@
--from import_tree import mod1
+-from import_tree import mod
 +from import_tree import renamedm
  #? 0 renamedm
--mod1
+-mod
 +renamedm