I think it's relevant to note that __clone is NOT an override. As the example shows, the normal cloning process always occurs, and it's the responsibility of the __clone method to "mend" any "wrong" action performed by it.

Here is test script i wrote to test the behaviour of clone when i have arrays with primitive values in my class - as an additonal test of the note below by jeffrey at whinger dot nl

<pre>
<?php

class MyClass {

    private $myArray = array();
    function pushSomethingToArray($var) {
        array_push($this->myArray, $var);
    }
    function getArray() {
        return $this->myArray;
    }

}

//push some values to the myArray of Mainclass
$myObj = new MyClass();
$myObj->pushSomethingToArray('blue');
$myObj->pushSomethingToArray('orange');
$myObjClone = clone $myObj;
$myObj->pushSomethingToArray('pink');

//testing
print_r($myObj->getArray());     //Array([0] => blue,[1] => orange,[2] => pink)
print_r($myObjClone->getArray());//Array([0] => blue,[1] => orange)
//so array  cloned 

?>
</pre>

I ran into the same problem of an array of objects inside of an object that I wanted to clone all pointing to the same objects. However, I agreed that serializing the data was not the answer. It was relatively simple, really:

public function __clone() {
    foreach ($this->varName as &$a) {
        foreach ($a as &$b) {
            $b = clone $b;
        }
    }
}

Note, that I was working with a multi-dimensional array and I was not using the Key=>Value pair system, but basically, the point is that if you use foreach, you need to specify that the copied data is to be accessed by reference.

Another gotcha I encountered: like __construct and __desctruct, you must call parent::__clone() yourself from inside a child's __clone() function. The manual kind of got me on the wrong foot here: "An object's __clone() method cannot be called directly."

Here are some cloning and reference gotchas we came up against at Last.fm.

1. PHP treats variables as either 'values types' or 'reference types', where the difference is supposed to be transparent. Object cloning is one of the few times when it can make a big difference. I know of no programmatic way to tell if a variable is intrinsically a value or reference type. There IS however a non-programmatic ways to tell if an object property is value or reference type:

<?php

class A { var $p; }

$a = new A;
$a->p = 'Hello'; // $a->p is a value type
var_dump($a);

/*
object(A)#1 (1) {
  ["p"]=>
  string(5) "Hello" // <-- no &
}
*/

$ref =& $a->p; // note that this CONVERTS $a->p into a reference type!!
var_dump($a);

/*
object(A)#1 (1) {
  ["p"]=>
  &string(5) "Hello" // <-- note the &, this indicates it's a reference.
}
*/

?>

2. unsetting all-but-one of the references will convert the remaining reference back into a value. Continuing from the previous example:

<?php

unset($ref);
var_dump($a);

/*
object(A)#1 (1) {
  ["p"]=>
  string(5) "Hello"
}
*/

?>

I interpret this as the reference-count jumping from 2 straight to 0. However...

2. It IS possible to create a reference with a reference count of 1 - i.e. to convert an property from value type to reference type, without any extra references. All you have to do is declare that it refers to itself. This is HIGHLY idiosyncratic, but nevertheless it works. This leads to the observation that although the manual states that 'Any properties that are references to other variables, will remain references,' this is not strictly true. Any variables that are references, even to *themselves* (not necessarily to other variables), will be copied by reference rather than by value. 

Here's an example to demonstrate:

<?php

class ByVal
{
    var $prop;
}

class ByRef
{
    var $prop;
    function __construct() { $this->prop =& $this->prop; }
}

$a = new ByVal;
$a->prop = 1;
$b = clone $a;
$b->prop = 2; // $a->prop remains at 1

$a = new ByRef;
$a->prop = 1;
$b = clone $a;
$b->prop = 2; // $a->prop is now 2

?>

This base class automatically clones attributes of type object or array values of type object recursively. Just inherit your own classes from this base class.

<?php
    class clone_base
    {
        public function __clone()
        {
            $object_vars = get_object_vars($this);

            foreach ($object_vars as $attr_name => $attr_value)
            {
                if (is_object($this->$attr_name))
                {
                    $this->$attr_name = clone $this->$attr_name;
                }
                else if (is_array($this->$attr_name))
                {
                    // Note: This copies only one dimension arrays
                    foreach ($this->$attr_name as &$attr_array_value)
                    {
                        if (is_object($attr_array_value))
                        {
                            $attr_array_value = clone $attr_array_value;
                        }
                        unset($attr_array_value);
                    }
                }
            }
        }
    }
?>

Example:
<?php
    class foo extends clone_base
    {
        public $attr = "Hello";
        public $b = null;
        public $attr2 = array();

        public function __construct()
        {
            $this->b = new bar("World");
            $this->attr2[] = new bar("What's");
            $this->attr2[] = new bar("up?");
        }
    }

    class bar extends clone_base
    {
        public $attr;

        public function __construct($attr_value)
        {
            $this->attr = $attr_value;
        }
    }

    echo "<pre>";

    $f1 = new foo();
    $f2 = clone $f1;
    $f2->attr = "James";
    $f2->b->attr = "Bond";
    $f2->attr2[0]->attr = "Agent";
    $f2->attr2[1]->attr = "007";

    echo "f1.attr = " . $f1->attr . "\n";
    echo "f1.b.attr = " . $f1->b->attr . "\n";
    echo "f1.attr2[0] = " . $f1->attr2[0]->attr . "\n";
    echo "f1.attr2[1] = " . $f1->attr2[1]->attr . "\n";
    echo "\n";
    echo "f2.attr = " . $f2->attr . "\n";
    echo "f2.b.attr = " . $f2->b->attr . "\n";
    echo "f2.attr2[0] = " . $f2->attr2[0]->attr . "\n";
    echo "f2.attr2[1] = " . $f2->attr2[1]->attr . "\n";
?>

Here is a basic example about clone issue. If we use clone in getClassB method. Return value will be same as new B() result. But it we dont use clone we can effect B::$varA. 

class A 
{
    protected $classB;
    
    public function __construct(){
        $this->classB = new B();
    }
    
    public function getClassB()
    {
        return clone $this->classB;
    }
}

class B
{
    protected $varA = 2;
    
    public function getVarA()
    {
        return $this->varA;
    }
    
    public function setVarA()
    {
        $this->varA = 3;
    }
}

$a = new A();

$classB = $a->getClassB();

$classB->setVarA();

echo $a->getClassB()->getVarA() . PHP_EOL;// with clone -> 2, without clone it returns -> 3

echo $classB->getVarA() . PHP_EOL; // returns always 3

It should go without saying that if you have circular references, where a property of object A refers to object B while a property of B refers to A (or more indirect loops than that), then you'll be glad that clone does NOT automatically make a deep copy!

<?php

class Foo
{
    var $that;

function __clone()
{
    $this->that = clone $this->that;
}

}

$a = new Foo;
$b = new Foo;
$a->that = $b;
$b->that = $a;

$c = clone $a;
echo 'What happened?';
var_dump($c);

PHP 8.5 introduces a new clone() syntax that streamlines the common situation of wanting a clone but with some of the properties changed.

Writing $copy = clone($obj, ['field'] => $value) will make $copy a clone of $obj except that $copy->field will equal $value instead of whatever $obj->field was.

<?php

class Thingy
{
    public int $a;
    public int $b;
    // ..... etc. etc.
}

$foo = new Thingy;
$foo->a = 17;
$foo->b = 42;
// ... etc. etc.

$bar = clone($foo, ['a' => 0]);

echo "{$foo->a} {$foo->b} ...\n";
echo "{$bar->a} {$bar->b} ...\n";
?>

It's possible to know how many clones have been created of a  object. I'm think that is correct:

<?php

class Classe {

    public static $howManyClones = 0;

    public function __clone() {
        ++static::$howManyClones;
    }

    public static function howManyClones() {
        return static::$howManyClones;
    }

    public function __destruct() {
        --static::$howManyClones;
    }
}

$a = new Classe;

$b = clone $a;
$c = clone $b;
$d = clone $c;

echo 'Clones:' . Classe::howManyClones() . PHP_EOL;

unset($d);

echo 'Clones:' . Classe::howManyClones() . PHP_EOL;

It's clearly depicted in the manual, about the mechanism of clone process:
- First, shallow copy: properties of references will keep references (refer to the same target/variable)
- Then, change content/property as requested (calling __clone method which is defined by user).

To illustrate this process, the following example codes seems better, comparing the the original version:

class SubObject
{
    static $num_cons = 0;
    static $num_clone = 0;

    public $construct_value;
    public $clone_value;

    public function __construct() {
        $this->construct_value = ++self::$num_cons;
    }

    public function __clone() {
        $this->clone_value = ++self::$num_clone;
    }
}

class MyCloneable
{
    public $object1;
    public $object2;

    function __clone()
    {
        // 强制复制一份this->object， 否则仍然指向同一个对象
        $this->object1 = clone $this->object1;
    }
}

$obj = new MyCloneable();

$obj->object1 = new SubObject();
$obj->object2 = new SubObject();

$obj2 = clone $obj;

print("Original Object:\n");
print_r($obj);
echo '<br>';
print("Cloned Object:\n");
print_r($obj2);

==================

the output is as below

Original Object:
MyCloneable Object
(
    [object1] => SubObject Object
        (
            [construct_value] => 1
            [clone_value] => 
        )

    [object2] => SubObject Object
        (
            [construct_value] => 2
            [clone_value] => 
        )

)
<br>Cloned Object:
MyCloneable Object
(
    [object1] => SubObject Object
        (
            [construct_value] => 1
            [clone_value] => 1
        )

    [object2] => SubObject Object
        (
            [construct_value] => 2
            [clone_value] => 
        )

)