The bug is filed here: bugs.launchpad.net/…ug/1244338
and here: bugzilla.gnome.org/…ow_bug.cgi
but if you can’t wait for the fix to come down from upstream, you can simply run this code as root:
EXT='/usr/lib/x86_64-linux-gnu/gedit/plugins/externaltools/functions.py' #for 64-bit systems
EXT='/usr/lib/i386-linux-gnu/gedit/plugins/externaltools/functions.py' #for 32-bit systems
mv $EXT $EXT.sav
sed -e 's%if doc.get_modified()%if not doc.get_modified()%' \
-e 's%for i in range(len(docs)):%for i in reversed(range(len(docs))):%' \
$EXT.sav > $EXT
EXT='/usr/lib/x86_64-linux-gnu/gedit/plugins/externaltools/functions.py' #for 64-bit systems
EXT='/usr/lib/i386-linux-gnu/gedit/plugins/externaltools/functions.py' #for 32-bit systems
rm -f $EXT.sav
mv $EXT $EXT.sav
sed -e 's%len(docs) and len(docs)%len(window.get_documents()) and len(docs_to_save)%' \
$EXT.sav > $EXT