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I don't know if the problem I had is the same, but when I wanted to use a custom template for cbb3.08 with in my theme, I noticed everything would show my templates all but the thread.html one. Taking a look at the veiwtopic.php I noticed this...
if($xoopsTpl->xoops_canUpdateFromFile() && is_dir(XOOPS_THEME_PATH."/".$xoopsConfig['theme_set']."/templates/".$xoopsModule->getVar("dirname"))){
$xoopsTpl->assign('newbb_template_path', XOOPS_THEME_PATH."/".$xoopsConfig['theme_set']."/templates/".$xoopsModule->getVar("dirname"));
}else{
$xoopsTpl->assign('newbb_template_path', XOOPS_ROOT_PATH."/modules/".$xoopsModule->getVar("dirname")."/templates");
}
I changed the templates to modules
if($xoopsTpl->xoops_canUpdateFromFile() && is_dir(XOOPS_THEME_PATH."/".$xoopsConfig['theme_set']."/modules/".$xoopsModule->getVar("dirname"))){
$xoopsTpl->assign('newbb_template_path', XOOPS_THEME_PATH."/".$xoopsConfig['theme_set']."/modules/".$xoopsModule->getVar("dirname"));
}else{
$xoopsTpl->assign('newbb_template_path', XOOPS_ROOT_PATH."/modules/".$xoopsModule->getVar("dirname")."/templates");
}
Once I made that change, thread.html was being used from my themes directory not my module directory.