diff -Nru apt-clone-0.2.2ubuntu2/apt_clone.py apt-clone-0.2.2ubuntu3/apt_clone.py
--- apt-clone-0.2.2ubuntu2/apt_clone.py	2012-08-09 20:09:45.000000000 +0000
+++ apt-clone-0.2.2ubuntu3/apt_clone.py	2012-12-14 23:23:18.000000000 +0000
@@ -207,16 +207,20 @@
             tar.add(p, arcname="./etc/apt/trusted.gpg.d")
 
     def _write_state_sources_list(self, tar, scrub=False):
-        self._add_file_to_tar_with_password_check(tar,
-            apt_pkg.config.find_file("Dir::Etc::sourcelist"), scrub)
+        sources_list = apt_pkg.config.find_file("Dir::Etc::sourcelist")
+        self._add_file_to_tar_with_password_check(tar, sources_list, scrub,
+            "./etc/apt/sources.list")
         source_parts = apt_pkg.config.find_dir("Dir::Etc::sourceparts")
         if os.path.exists(source_parts):
+            tar.add(source_parts, arcname="./etc/apt/sources.list.d",
+                    recursive=False)
             for source in os.listdir(source_parts):
                 sources_file_name = '%s/%s' % (source_parts, source)
                 self._add_file_to_tar_with_password_check(tar,
-                    sources_file_name, scrub)
+                    sources_file_name, scrub,
+                    "./etc/apt/sources.list.d/"+source)
 
-    def _add_file_to_tar_with_password_check(self, tar, sources, scrub=False):
+    def _add_file_to_tar_with_password_check(self, tar, sources, scrub, arcname):
         if scrub:
             with tempfile.NamedTemporaryFile(mode='w') as source_copy:
                 with open(sources, 'r') as f:
@@ -228,9 +232,9 @@
                         else:
                             source_copy.write(line)
                         source_copy.flush()
-                    tar.add(source_copy.name, arcname=".%s" % (sources))
+                    tar.add(source_copy.name, arcname=arcname)
         else:
-            tar.add(sources, arcname='.%s' % sources)
+            tar.add(sources, arcname=arcname)
 
     def _write_modified_files_from_etc(self, tar):
         #etcdir = os.path.join(apt_pkg.config.get("Dir"), "etc")
diff -Nru apt-clone-0.2.2ubuntu2/debian/changelog apt-clone-0.2.2ubuntu3/debian/changelog
--- apt-clone-0.2.2ubuntu2/debian/changelog	2012-08-09 20:11:25.000000000 +0000
+++ apt-clone-0.2.2ubuntu3/debian/changelog	2012-12-14 23:24:55.000000000 +0000
@@ -1,3 +1,11 @@
+apt-clone (0.2.2ubuntu3) precise-proposed; urgency=low
+
+  * Ensure that /etc/apt/sources.list and /etc/apt/sources.list.d are put
+    at the right place in the tarball by hardcoding their location in the
+    tarball. (LP: #1066347) Thanks to Stéphane Graber for the patch.
+
+ -- Brian Murray <brian@ubuntu.com>  Fri, 14 Dec 2012 15:24:02 -0800
+
 apt-clone (0.2.2ubuntu2) precise-proposed; urgency=low
 
   * apt_clone.py: fix with syntax to work with python2.6 
diff -Nru apt-clone-0.2.2ubuntu2/tests/data/mock-system/etc/apt/sources.list.d/ubuntu-mozilla-daily-ppa-maverick.list apt-clone-0.2.2ubuntu3/tests/data/mock-system/etc/apt/sources.list.d/ubuntu-mozilla-daily-ppa-maverick.list
--- apt-clone-0.2.2ubuntu2/tests/data/mock-system/etc/apt/sources.list.d/ubuntu-mozilla-daily-ppa-maverick.list	2012-08-09 20:08:32.000000000 +0000
+++ apt-clone-0.2.2ubuntu3/tests/data/mock-system/etc/apt/sources.list.d/ubuntu-mozilla-daily-ppa-maverick.list	2012-12-14 23:21:38.000000000 +0000
@@ -1,6 +1,3 @@
-#disabled on upgrade to natty disabled on upgrade to natty
-# deb http://ppa.launchpad.net/ubuntu-mozilla-daily/ppa/ubuntu/ natty main
-#disabled on upgrade to natty disabled on upgrade to natty
-# deb-src http://ppa.launchpad.net/ubuntu-mozilla-daily/ppa/ubuntu/ natty main
+deb http://ppa.launchpad.net/ubuntu-mozilla-daily/ppa/ubuntu/ lucid main
 
 
diff -Nru apt-clone-0.2.2ubuntu2/tests/test_clone.py apt-clone-0.2.2ubuntu3/tests/test_clone.py
--- apt-clone-0.2.2ubuntu2/tests/test_clone.py	2012-08-09 20:08:32.000000000 +0000
+++ apt-clone-0.2.2ubuntu3/tests/test_clone.py	2012-12-14 23:26:11.000000000 +0000
@@ -10,10 +10,7 @@
 import tempfile
 import unittest
 
-from StringIO import StringIO
-
-sys.path.insert(0, "..")
-import apt_clone
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
 from apt_clone import AptClone
 
 class MockAptCache(apt.Cache):
@@ -25,6 +22,11 @@
 class TestClone(unittest.TestCase):
 
     def setUp(self):
+        #clean custom apt config
+        for d in apt_pkg.config.keys():
+            apt_pkg.config.clear(d)
+        apt_pkg.init_config()
+        # clean
         apt_pkg.config.set("Dir", "/")
         apt_pkg.config.set("dir::state::status", "/var/lib/dpkg/status")
         self.tempdir = tempfile.mkdtemp("apt-clone-tests")
@@ -71,6 +73,12 @@
         self.assertTrue("./etc/apt/preferences" in members)
         if clone.not_downloadable:
             self.assertEqual(clone.commands.repack_deb.called, with_dpkg_repack)
+        # ensure we have no duplicates in the sources.list.d
+        sources_list_d = [p for p in members 
+                          if p.startswith("./etc/apt/sources.list.d")]
+        self.assertCountEqual(sources_list_d,
+                ['./etc/apt/sources.list.d', 
+                 './etc/apt/sources.list.d/ubuntu-mozilla-daily-ppa-maverick.list'])
 
     @mock.patch("apt_clone.LowLevelCommands")
     def test_restore_state(self, mock_lowlevel):