This bug was fixed in the package gtk-doc - 1.17-0ubuntu1

---------------
gtk-doc (1.17-0ubuntu1) natty; urgency=low

  * New upstream release
  * Fix builds where srcdir != builddir (LP: #762567)
 -- Robert Ancell <robert.anc...@canonical.com>   Sat, 16 Apr 2011 18:09:29 
+1000

** Changed in: gtk-doc (Ubuntu)
       Status: New => Fix Released

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https://bugs.launchpad.net/bugs/762567

Title:
  gtk-doc-tools doesn't work when srcdir != builddir

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