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The problem is with Hooks.php, the event-handling mechanism for
optional functionality and third-party extensions. wfRunHooks(), the
interface for mainline code to raise events for hooks to handle,
uses PHP's variable-argument syntax. This is so you can give different
parameter sets to different events:

    wfRunHooks('Event1', $param1, $param2, $param3); # three params
    wfRunHooks('Event2', $param4, $param5); # just two params

The problem with this is that the var args syntax silently changes
pass-by-reference semantics to pass-by-value semantics. So events that
should allow modifying parameters do not. For example:

    $wgEventHooks['Event3'][] = 'MyEvent3Handler';
    # ...
    function MyEvent3Handler(&$str) {
        $str .= " and so on.";
        return true;
        }
    # ...
    $somestring = "Eggs, bananas, bacon";
    # NOTE: OLD CALLING FORMAT
    if (wfRunHooks('Event3', &$somestring)) {
        echo $somestring; # prints "Eggs, bananas, bacon"
    }

After some consulting with PHP gurus, the best solution I could come up
with was to pack the params in an array when passing them to
wfRunHooks(). Now the last few lines are:

    if (wfRunHooks('Event3', array(&$somestring))) {
        echo $somestring; # prints "Eggs, bananas, bacon and so on."
    }

Adding a reference to an array keeps its "reference-ness". Note that there's no
change to the (extension-located) hook function, just to the core code calling
conventions.

The above change has been implemented in HEAD; it needs to be ported to REL1_4.
(It was implemented and tested in REL1_4 originally, then moved to HEAD at the
request of vibber).