Here are some scattered modifications I've also done in v3.3.2f2:

1.
old:
MarkUp('fmt', 'indent', '/\-(&gt;|>)\n?/', '<blockquote>'); // -> <-
indent (blockquote)
MarkUp('fmt', 'indentend', '/\n?(&lt;|<)\-/', '</blockquote>'); // ->
<- indent (blockquote)

new:
MarkUp('fmt', 'indent', '/\-\&gt;\n?/', '<blockquote>'); // -> <-
indent (blockquote)
MarkUp('fmt', 'indentend', '/\n?&lt;\-/', '</blockquote>'); // -> <-
indent (blockquote)

2.
deleted the line in BOLTsearchPageList.
It is useless because we just done explode(',') so no comma should
exist at that time.
$p = str_replace(',', '|', $p);

3. removed the line below, and &query and $lastquery from globals in
BOLTdomarkup, if the modification of [messages] and [results] are done
as I mentioned previously:
        if ($content == '[results]' && $query == '' && $lastquery == '')
return;

4. In BOLTexecute
delete:
$auth = BOLTexists('site.auth.commands');

change:
                        if ($auth == false) $value = $BOLTcommand($value, 
$field);
                        elseif (BOLTauth($pageLink, $command, 'commands')) 
$value =
$BOLTcommand($value, $field);
to:
                        if (BOLTauth($pageLink, $command, 'commands', false)) 
$value =
$BOLTcommand($value, $field);

Just to simplify the code, since if site.auth.commands doesn't exist
the BOLTauth would always return true.
But it may slightly decrease the performance.
If you do this, do the same for BOLTfunc.
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