There is simplesect used which messes the ToC. According to Norman Walsh comment on simplesect it aren't supposed to be in ToC. Was it the main idea when writing en/install/pecl.xml? Should I alter XML or processing templates?
It is probably better to be conformant to DocBook guidelines, so fix the XML please. If it breaks translations (ie. you need to modify the container, but not only the XML file itself), then it is more work (it would be nice to fix it across translations). If it does not break the build, then there is no immediate need to fix the translated files.
Goba
