The picture is not large enough to really see the issue, even if you " (Click the thumbnail please)".

Thanks, I try hard to keep the image sizes down to save bandwidth and disk space. I won't be able to post another picture today. Maybe a little more narrative will help. If not, I will need some guidance to help me take a picture that shows what you need.

Here is what is in the pic from the top

White: door
black: soft weatherstrip of the threshold
gold: metal part of threshold
brown:edge of the flooring
Gray: Recently-painted riginal door sill if "sill" is the right word
Mottled gray-green: concrete porch deck that I have not yet had time to paint.

Oh, wait, I do have a wider shot if that helps.

(shakes head in disbelief) You have got to be kidding. Somebody got paid to do this to your house?
Someone needed to point out that previous layers of flooring had to be removed so the new flooring was no higher than the original door sill. Removal costs more dough, but this is just a fustercluck now.
Casey

You almost have it. The LR was down to the joists and plywood went on top of that. I think that they raised that a little so it would be level into other rooms where the subfloor was higher for some reason.

Before this project started, the LR, where the pictured door is, was tongue and groove. The hallway from the LR and one BR, that connected to that hallway were carpet over plywood. I won't go into details about the layers of whatnot flooring in other rooms.

Yes, I pay people all the time to ruin my house. After that is a pile of junk, we can start on the garage!

Seriously now, at first I was hoping that they were not finished. After a time, I realized that there is probably no way to "finish" this without tearing it apart and starting over.

How should this be fixed? The threshold is supposed to sit on top of the engineered flooring, right? What should happen now?

Does the threshold come out and the sill get replaced and the threshold get put back on?

Does the threshold come out and the sill, if sound, get added to so it is high enough?

Something else?

I suppose that I could just demand that the contractor get a real carpenter and let him figure it out. I'd like to know how it is supposed to be done rather than just point point to it and say , "this does not look right and I don't think that caulk is going to fix it."

I've been looking for a good picture or diagram of how the underparts of a doorway are assembled in a frame house with little luck.

Silly me, the unfinished wood under the threshold is not flooring. I should have looked more closely at it.