Eagle: PCB layers stack-up and impedance
The PCB manufacturer is asking for the stack-up because  generally people include Power planes and Ground planes in between the layers. 
So how would the PCB manufacturer know where to put which layer?

Sophisticated PCB Manufacturers also have impedance control on signals. You should provide him the stack file. 
Like USB Differential Signals (D+ and D-) require impedance control on tracks. AFAIK, 90 ohm to be exact. 

He requires these files for quality manufacturing.