This bug was fixed in the package apt-clone - 0.3.1~ubuntu3

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apt-clone (0.3.1~ubuntu3) raring; urgency=low

  * Do not include subdirectories in /etc/apt/sources.list.d/ (LP: #1077113)
 -- Brian Murray <br...@ubuntu.com>   Fri, 25 Jan 2013 13:47:56 -0800

** Changed in: apt-clone (Ubuntu)
       Status: New => Fix Released

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https://bugs.launchpad.net/bugs/1077113

Title:
  do-release-upgrade crashes if any directories exist in
  /etc/apt/sources.list.d

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