unless you really, really have to. I did some quick Googling on this and found that a number of places recommend making changes to index.php.
In my humble opinion it is better to leave the index.php file alone and configure your stores via SetEnv in your Apache config, as is noted in the Magento wiki.
For example
<VirtualHost *:80>
SetEnv MAGE_RUN_CODE msv
ServerName kps.loc
DocumentRoot /var/www/magento.loc/magento
CustomLog logs/magento.access_log varnishcombined
ErrorLog logs/magento.error_log
</VirtualHost>
<VirtualHost *:80>
SetEnv MAGE_RUN_CODE base
ServerName magento.loc
DocumentRoot /var/www/magento.loc/magento
CustomLog logs/magento.access_log varnishcombined
ErrorLog logs/magento.error_log
</VirtualHost>
No code changes required and upgrades won’t break your modifications.
That is all.
