calculation of phi
 

Where do I have to look (in the source code), if I want to know how phi is calculated in interFoam?

In createFields.H, you'll see the line include "createPhi.H". You can find this in OpenFOAM-1.X/src/finiteVolume/cfdTools/incompressible

It is defined as:

phi = linearInterpolate(U) & mesh.Sf()

I think the best thing to do is to set up your IDE's code assistance, so that you can easily navigate through the source code.

If phi is calculated from U, what is the advantage of using boundary conditions like fluxCorrectedVelocity, pressureInletVelocity, pressureInletOutletVelocity - which calculate U form the flux(phi)?

I've had a quick look at fluxCorrectedVelocity.
It would be used when you know the pressure at a boundary and the flux through that boundary.
The BC is correcting the velocity component normal to the boundary, based on your knowledge of the flux through that boundary.
I can't think of when I would use it, maybe someone else has?

You could replace all instances of phi with linearInterpolate(U) & mesh.Sf(), but that would make the code messy.