MalformedTransform: Tree transform is malformed [('versioning no contents', 'new-126')]

Some of my patches create files from scratch, my fuzzy feeling is that 'missing/removed' files choke bzr, since they were modified on the other side.

Workaround:
Use these settings
[BUILDDEB]
commit-message-from-changelog=True
quilt-tree-policy=unapplied
quilt-commit-policy=unapplied
quilt-smart-merge=True
and do $ quilt pop -a && bzr commit -m 'do a pop all'

$ bzr branch lp:~dmitrij.ledkov/ubuntu/quantal/mdadm/bzr-bug-source sid
$ bzr branch lp:~dmitrij.ledkov/ubuntu/quantal/mdadm/bzr-bug-target quantal
$ cd quantal/
$ bzr merge ../sid/
Unapplying quilt patches to prevent spurious conflicts
bzr: ERROR: bzrlib.errors.MalformedTransform: Tree transform is malformed [('versioning no contents', 'new-126')]

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 920, in exception_to_return_code
    return the_callable(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 1131, in run_bzr
    ret = run(*run_argv)
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 673, in run_argv_aliases
    return self.run(**all_cmd_args)
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 695, in run
    return self._operation.run_simple(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 136, in run_simple
    self.cleanups, self.func, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 166, in _do_with_cleanups
    result = func(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/builtins.py", line 4446, in run
    verified)
  File "/usr/lib/python2.7/dist-packages/bzrlib/builtins.py", line 4465, in _do_merge
    conflict_count = merger.do_merge()
  File "/usr/lib/python2.7/dist-packages/bzrlib/merge.py", line 686, in do_merge
    merge = operation.run_simple()
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 136, in run_simple
    self.cleanups, self.func, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 166, in _do_with_cleanups
    result = func(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/merge.py", line 654, in _do_merge_to
    merge.do_merge()
  File "/usr/lib/python2.7/dist-packages/bzrlib/merge.py", line 802, in do_merge
    operation.run()
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 132, in run
    self.cleanups, self.func, self, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 166, in _do_with_cleanups
    result = func(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/merge.py", line 807, in _do_merge
    self._compute_transform()
  File "/usr/lib/python2.7/dist-packages/bzrlib/merge.py", line 857, in _compute_transform
    self._finish_computing_transform()
  File "/usr/lib/python2.7/dist-packages/bzrlib/merge.py", line 867, in _finish_computing_transform
    lambda t, c: transform.conflict_pass(t, c, self.other_tree))
  File "/usr/lib/python2.7/dist-packages/bzrlib/transform.py", line 3033, in resolve_conflicts
    raise MalformedTransform(conflicts=conflicts)
MalformedTransform: Tree transform is malformed [('versioning no contents', 'new-126')]

bzr 2.5.0 on python 2.7.3 (Linux-3.4.0-5-generic-x86_64-with-
    Ubuntu-12.10-quantal)
arguments: ['/usr/bin/bzr', 'merge', '../sid/']
plugins: automv[unknown], bash_completion[2.5.0], builddeb[2.7.0dev],
    builder[0.7.2dev], bzrtools[2.5.0], changelog_merge[2.5.0],
    dbus[0.1.0dev], etckeeper[unknown], explorer[1.3.0dev], git[0.6.8dev],
    grep[0.5.0dev], gtk[0.104.0dev], launchpad[2.5.0],
    netrc_credential_store[2.5.0], news_merge[2.5.0], pipeline[1.4.0],
    po_merge[2.5.0], qbzr[0.22.2], rewrite[0.6.4dev], svn[1.2.2dev],
    weave_fmt[2.5.0]
encoding: 'utf-8', fsenc: 'UTF-8', lang: 'en_GB.UTF-8'

*** Bazaar has encountered an internal error. This probably indicates a
    bug in Bazaar. You can help us fix it by filing a bug report at
        https://bugs.launchpad.net/bzr/+filebug
    including this traceback and a description of the problem.