That actually has 2 in, 1 out.
Left hand side of shot, the air filter intake
4/5 of the way across, that is the Blow off valve recirculation (air IN) to work with your standard setup.
and the turbo inlet (OUT)
That solenoid controls your actuator, the bit which controls the boost your turbo is producing by operating a wastegate inside the turbo. It gets swapped out if you get any aftermarket boost control like an Apexi AVCR
To tell you the truth I can't remember exactly what will happen if you ditch that nipple, it would probably be bad.
To retain the stock system with your new pipe fit one of these to the silicone joiner closer to the turbo
http://www.ebay.co.uk/itm/Tdi-diese...arts_Vehicles_CarParts_SM&hash=item2a306c5a4c
Just make sure you get the right size, it isn't being squashed from the turbo on one side, or the pipe on the other, and it doesn't leak!!