[HurrdurrHodor]

"Trace the flow of data from client to network to app to disk to app to network to client etc."

How would one go about doing that?

[ChuckMcM]

In the ideal world? With a copy of the full schematic, a datasheet for the SoC, and source code to the kernel and drivers. Its harder with RasPi because various bits are obscured but many of the drivers are open enough to figure much of it out.