When running the Magento readiness test it failed with the message that always_populate_raw_post_data should be set to -1 since it is running under php 5.6. Even though I tried different methods of setting it to -1 and I could verify it by calling phpinfo(); Magento still complained.
The way I solved is a bit rough and it required that I had full system administrator access to the machine (which I had because it was a dedicated server). This is how I solved it:
echo "always_populate_raw_post_data=-1" > /etc/php5/mods-available/always_populate_raw_post_data.ini
service php5-fpm restart
service apache2 restart