We had a spray foam roof put on our 35 year old house last year. We now have a leak below a bank of clerestory windows.  Days of hose testing revealed that water is entering below the sloped window sill where the underside of the sill meets the exterior wall.  

The last time the roofer was here about the leak, he met with a local window installer.  The installer said that the junction where the underside of the sill meets the exterior wall should have a small gap that functions like a weep hole. He had the roofer leave a very thin linear gap the length of each window’s sill. The windows were installed 10 years ago, but the manufacturer no longer has a presence here; he is not the original installer.

In this region, we get driving rains that come straight toward those windows.  I know there are windows with weep holes and windows with sloped sills for drainage, but are we really not supposed to seal below the window sill?  

Please see attached photo to see where this gap is.  The roofer made numerous mistakes on this part of the roof, and it looks like ***.  Please focus your comments, though, on the question of the linear gap and on how we might fix this.  This is a southwestern US stucco house with a slightly sloped, flat roof.

Thank you.