Can you please provide a reproducible case as a short PHP script?

It seems I may not have properly described the issue at first. I noticed this happening to code someone else had written, and it was part of a massive library. It took many hours of trial and error to rewrite this library as a "short" PHP script, such that it still had the same discrepancy between PHP 5.6.0 and Master.

Test script:
####
$arr = array(
	'a' => array(
		'a' => 'apple',
		'b' => 'banana',
		'c' => 'cranberry',
		'd' => 'mango',
		'e' => 'pineapple'
	),
	'b' => array(
		'a' => 'apple',
		'b' => 'banana',
		'c' => 'cranberry',
		'd' => 'mango',
		'e' => 'pineapple'
	),
	'c' => 'cranberry',
	'd' => 'mango',
	'e' => 'pineapple'
);

function test(&$child, $entry)
{
	$i = 1;

	foreach ($child AS $key => $fruit)
	{
		if (!is_numeric($key))
		{
			$child[$i] = $fruit;
			unset($child[$key]);
			$i++;
		}
	}
}

$i = 1;

foreach ($arr AS $key => $fruit)
{
	$arr[$i] = $fruit;

	if (is_array($fruit))
	{
		test($arr[$i], $fruit);
	}

	unset($arr[$key]);
	$i++;
}

var_dump($arr);
####
Expect: In 5.6, this re-keys a,b,c,d,e at all array levels as 1,2,3,4,5 respectively.
Actual: In Master, this re-keys correctly on the outer-most level. On the second level, only a,b,c,d is re-keyed.

Notes: This has something to do with the reference in the definition for function test. If we break the reference within the function, then Master replicates the expected 5.6 behavior:
####
function test(&$child, $entry)
{
	$i = 1;
	$tmp = $child;

	foreach ($tmp AS $key => $fruit)
	{
		if (!is_numeric($key))
		{
			$child[$i] = $fruit;
			unset($child[$key]);
			$i++;
		}
	}
}
####

Test script provided above.

Yes, looks like a problem in master:

http://3v4l.org/XrVYT