diff -Nru bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/bzrlib/config.py bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/bzrlib/config.py
--- bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/bzrlib/config.py	2014-05-08 10:18:11.000000000 +0000
+++ bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/bzrlib/config.py	2014-06-20 15:36:25.000000000 +0000
@@ -3559,7 +3559,6 @@
         """
         location_parts = self.location.rstrip('/').split('/')
         store = self.store
-        sections = []
         # Later sections are more specific, they should be returned first
         for _, section in reversed(list(store.get_sections())):
             if section.id is None:
@@ -4246,6 +4245,8 @@
     def _set_config_option(self, name, value, directory, scope):
         conf = self._get_stack(directory, scope, write_access=True)
         conf.set(name, value)
+        # Explicitly save the changes
+        conf.store.save_changes()
 
     def _remove_config_option(self, name, directory, scope):
         if name is None:
@@ -4254,6 +4255,8 @@
         conf = self._get_stack(directory, scope, write_access=True)
         try:
             conf.remove(name)
+            # Explicitly save the changes
+            conf.store.save_changes()
         except KeyError:
             raise errors.NoSuchConfigOption(name)
 
diff -Nru bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/debian/bzr-builder.manifest bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/debian/bzr-builder.manifest
--- bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/debian/bzr-builder.manifest	2014-05-08 10:18:11.000000000 +0000
+++ bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/debian/bzr-builder.manifest	2014-06-20 15:36:25.000000000 +0000
@@ -1,4 +1,4 @@
-# bzr-builder format 0.3 deb-version {debupstream-base}bzr6597.6324~ppa4079
-lp:bzr revid:pqm@pqm.ubuntu.com-20140508025629-de62pqrditrp349y
+# bzr-builder format 0.3 deb-version {debupstream-base}bzr6598.6324~ppa4079
+lp:bzr revid:pqm@pqm.ubuntu.com-20140620152437-lrczj6lnsbp1gpsl
 merge packaging lp:~debian-bazaar/bzr/2.6 revid:a.starr.b@gmail.com-20131008141212-ag9pr3l9qd4eggve
 merge translations lp:~bzr-core/bzr/bzr-translations-export revid:launchpad_translations_on_behalf_of_bzr-core-20140409043047-9wd83jiedscu5lys
diff -Nru bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/debian/changelog bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/debian/changelog
--- bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/debian/changelog	2014-05-08 10:18:11.000000000 +0000
+++ bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/debian/changelog	2014-06-20 15:36:25.000000000 +0000
@@ -1,8 +1,8 @@
-bzr (2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1) saucy; urgency=low
+bzr (2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1) saucy; urgency=low
 
   * Auto build.
 
- -- Launchpad Package Builder <noreply@launchpad.net>  Thu, 08 May 2014 10:18:11 +0000
+ -- Launchpad Package Builder <noreply@launchpad.net>  Fri, 20 Jun 2014 15:36:25 +0000
 
 bzr (2.6.0+bzr6589-1) UNRELEASED; urgency=low
 
diff -Nru bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/doc/en/release-notes/bzr-2.7.txt bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/doc/en/release-notes/bzr-2.7.txt
--- bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/doc/en/release-notes/bzr-2.7.txt	2014-05-08 10:09:33.000000000 +0000
+++ bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/doc/en/release-notes/bzr-2.7.txt	2014-06-20 15:33:09.000000000 +0000
@@ -72,6 +72,11 @@
    suite.  This can include new facilities for writing tests, fixes to 
    spurious test failures and changes to the way things should be tested.
 
+* Fix warnings on stderr caused by the atexit handler triggering for the
+  wrong reason: the 'config' command should explicitly save the changes when
+  modifying or removing an option and not rely on the atexit
+  handler. (Vincent Ladeuil, #1331999)
+
 * Handle (minor) incompatible change in python 2.7.6 leading to test
   failures. Only tests are affected. (Vincent Ladeuil, #1303879)
 
diff -Nru bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/.pc/02_external_configobj/bzrlib/config.py bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/.pc/02_external_configobj/bzrlib/config.py
--- bzr-2.6.0+bzr6597.6324~ppa4079~ubuntu13.10.1/.pc/02_external_configobj/bzrlib/config.py	2014-05-08 10:09:33.000000000 +0000
+++ bzr-2.6.0+bzr6598.6324~ppa4079~ubuntu13.10.1/.pc/02_external_configobj/bzrlib/config.py	2014-06-20 15:33:09.000000000 +0000
@@ -3559,7 +3559,6 @@
         """
         location_parts = self.location.rstrip('/').split('/')
         store = self.store
-        sections = []
         # Later sections are more specific, they should be returned first
         for _, section in reversed(list(store.get_sections())):
             if section.id is None:
@@ -4246,6 +4245,8 @@
     def _set_config_option(self, name, value, directory, scope):
         conf = self._get_stack(directory, scope, write_access=True)
         conf.set(name, value)
+        # Explicitly save the changes
+        conf.store.save_changes()
 
     def _remove_config_option(self, name, directory, scope):
         if name is None:
@@ -4254,6 +4255,8 @@
         conf = self._get_stack(directory, scope, write_access=True)
         try:
             conf.remove(name)
+            # Explicitly save the changes
+            conf.store.save_changes()
         except KeyError:
             raise errors.NoSuchConfigOption(name)