Update phpdotenv to 1.0.9
Require PHP 5.4

Although there is no hard requirement on this, 5.3 should not be
"allowed" since it's reached end of life and isn't even supported
anymore.
Updates to default deploy.rb config

`linked_files` and `linked_dirs` updated to match official Capistrano
defaults. This allows plugins to set these variables as well.
fix merge