In general the files themselves should be fairly self explanatory. See the root README.md for details on linux/windows. As a brief breakdown:
- ap-gazebo - Starts the core gazebo simulator/arducopter/mavros/ros-web-bridge stack only. Recommended for low level use or use primarily with a GCS (QGC or Mission Planner).
- arducopter - Starts the arducopter sitl only with a simple mavlink bridge. Recommended for use with only a GCS.