I've added a QA warning to autotools.eclass so that now using its functions outside of src_unpack throws is reported to the users (and thus to the developers to fix it). I'm filing bugs for the packages I can easily find being doing this through a simple grep on the tree. If you fixed the issue in the last version of an ebuild and I still opened this bug, please don't close it until you removed that ebuild from the tree. Thanks for the cooperation.
Fixed in CVS
+*gedit-2.26.3-r1 (28 Oct 2009) + + 28 Oct 2009; Gilles Dartiguelongue <eva@gentoo.org> -gedit-2.26.2.ebuild, + +gedit-2.26.3-r1.ebuild, +files/gedit-2.26.3-external_tools_config.patch: + Version bump. Add patch to fix external tools plugin configuration dialog, + bug #207457. + Thanks for reporting.