<?php

class Inside {
    public $a = 1;
    public function setA($a){
        $this->a = $a;
    }
}

class Base {
     public $inside;
     public function __clone() {
         $this->inside = clone $this->inside;
     }
}

$base = new Base();
$base->inside = new Inside();

var_dump($base);

$clone = clone $base;

$base->inside->setA(2);

var_dump($clone);