logstash output to file and ignores codec

Parameter message_format is deprecated and will be remove in future relases of Logstash. Instead of using message_format try something like this:

file {
  codec => line {
    format => "%{[time]} | %{[severity]} : /%{[thread]}/ %{[loggername]} (%{[sourcemethodname]}) - %{[message]}"
  }
  path => "/Users/[some user]/logs/%{host}/%{facility}-%{+YYYY-MM-dd}.log"
}

PS: your example using codec plain, try my with line.

file has a message_format parameter that is what you'll want to use:

file {
  message_format => "%{[time]} | %{[severity]} : /%{[thread]}/ %{[loggername]} (%{[sourcemethodname]}) - %{[message]}"
  path => "/Users/[some user]/logs/%{host}/%{facility}-%{+YYYY-MM-dd}.log"
}