I have made a change to civilian detection to try and improve performance a little. At the moment, you have to detect your own civilians using your sensors. However, they have transponders so 99% of the time they are automatically detected anyway. So in v5.0, your civilian ships are always detected, just like civilian mining colonies. In fact they won't even really be contacts - they will show up like one of your own fleets but in the civilian contact colour. You can still hide them by turning off civilian contacts. The advantage of this is that the sensor and detection code won't even run for those systems where there are only your ships and civilian ships. This also means there won't be a civilian alien race because you will never actually detect them and civilian contacts won't clog up the various contact lists.
Steve