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PS2 = "... " is defined with a trailing space which is not stripped for empty lines with only PS2 in the doctest. A patch would be to strip the trailing space in PS2 for empty lines and a unittest would be as below. There are no test cases for this scenario asserting against exact format and hence the patch doesn't break any tests. Currently I don't see any doctest in the codebase having this leading whitespace. I can try converting this patch as PR if Benjamin is okay with the change.
diff --git a/Lib/lib2to3/refactor.py b/Lib/lib2to3/refactor.py
index 7841b99a5c..135678b46e 100644
--- a/Lib/lib2to3/refactor.py
+++ b/Lib/lib2to3/refactor.py
@@ -599,7 +599,11 @@ class RefactoringTool(object):
 new[-1] += "\n"
 block = [indent + self.PS1 + new.pop(0)]
 if new:
- block += [indent + self.PS2 + line for line in new]
+ for line in new:
+ if not line.strip():
+ block += [indent + self.PS2.strip() + line]
+ else:
+ block += [indent + self.PS2 + line]
 return block
 
 def summarize(self):
diff --git a/Lib/lib2to3/tests/test_refactor.py b/Lib/lib2to3/tests/test_refactor.py
index 9e3b8fbb90..f6a5e2d589 100644
--- a/Lib/lib2to3/tests/test_refactor.py
+++ b/Lib/lib2to3/tests/test_refactor.py
@@ -331,3 +331,22 @@ from __future__ import print_function"""
 break
 else:
 self.fail("explicit fixer not loaded")
+
+ def test_refactor_doctest(self):
+ rt = self.rt()
+
+ expected = """
+>>> class Foo():
+... def cheese(self):
+... pass
+...
+"""
+
+ doc = """
+>>> class Foo():
+... def parrot(self):
+... pass
+...
+"""
+ out = rt.refactor_docstring(doc, "<test>")
+ self.assertEqual(out, expected)
Without patch this fails as below : 
$ ./python.exe -m unittest -v lib2to3.tests.test_refactor.TestRefactoringTool.test_refactor_doctest
test_refactor_doctest (lib2to3.tests.test_refactor.TestRefactoringTool) ... FAIL
======================================================================
FAIL: test_refactor_doctest (lib2to3.tests.test_refactor.TestRefactoringTool)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/Users/karthikeyansingaravelan/stuff/python/cpython/Lib/lib2to3/tests/test_refactor.py", line 352, in test_refactor_doctest
 self.assertEqual(out, expected)
AssertionError: '\n>>> class Foo():\n... def cheese(self):\n... pass\n... \n' != '\n>>> class Foo():\n... def cheese(self):\n... pass\n...\n'
 >>> class Foo():
 ... def cheese(self):
 ... pass
- ...
? -
+ ...
----------------------------------------------------------------------
Ran 1 test in 0.032s
FAILED (failures=1)