[fix] PHP Deprecated warnings to work with php_beautifier

+ I have tried to fix PEAR issue with php beautifier.
+ When trying to format code using beautifier there below error is shown in Lunux ubuntu with Php 5.3.10-1ubuntu3.6

```
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 650
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 697
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 757
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 786
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 914
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 1577
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 1607
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 2038
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Config.php on line 2091
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Registry.php on line 322
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Registry.php on line 1450
PHP Deprecated:  Assigning the return value of new by reference is deprecated in /home/gunjan/pear/share/pear/PEAR/Registry.php on line 1458
```