Its a cold water supply to something in your home. Turn the valve off and see what it turns off. As for the pipe that they teed on the bottom where the boiler drain is. Only time I seen some one do that is a recirc return line.
One other alliterative is that they are taking running the two pipes to HVAC unit. If that is the case someone replaced the original heater with the wrong unit and plumbed it in crazy. With out being there and looking into things it is hard to tell what and why they plumbed it in the way they did.