Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and a better than average (for a layman) understanding of how DNA works.
I understand the process of Amino Acid being coded for by specific DNA nucleotides and the chains of Amino Acid forming specific proteins - however, I am unable to find information on the topic of how actual shape is determined / coded for by DNA (again, not Hox genes and body segments).
Here is an example of what I am asking about - please note that this is just an example and I'm not specifically asking about how eyes evolved. I'm asking how changes in shape/size/structure of any part of a body happens from changes in DNA.
It's generally held that eyes evolved (in very basic terms) from a layer of photosensitive cells on the skin, which slowly formed into a cup that could detect direction, then the cup eventually closing in to form a smaller hole, and then a lens, and so on.
So my question (based on that example), would be, how does DNA (or a change in DNA) code for "create an indentation on the surface of the skin at this location". Or, "Deepen the indentation repeatedly until it is a cup". And so on.
More basic examples are "make the hind legs on a mammal slightly longer" or "make the cranium on an ape slightly larger". The question is not dependent on body part or animal type but is specifically about how DNA, in general, operates.
Hopefully the question is clearly stated and not too long - I welcome any suggestions on how to clarify the question.
--added-- canadianer's comment gave excellent information regarding some general principles that are involved, but I'm still hoping to find (if it's possible) a more precise and detailed answer to this.