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It all begins with the polarity of the female egg. Gradients of gene products across the single cell. Then gradients of other gene products across multiple cells as they divide. This gets more and more complex as the fetus grows and shapes emerge. Also see "homeotic genes" and their role in developmental biology. Source: cloned some of those myself and tinkered with them in flies.
I would just add that it's a gradient of transcription factor(s), proteins that regulate production of other proteins. Some of the regulated proteins are other thranscription factors that create finer gradients, like repeated stripes of gradients. along the initial, single gradient. This can be repeated on multiple levels so that pretty much every point of the body has unique combination of transcription factors. This combination triggers all the other proteins, including structural that create the form of the body. and of course, all this doesn't just happen in 3D, but also changes with time. It's complicated.
For illustration and possible direction for some particular interesting cases wrapped in a very entertaining package, I recommend this: https://www.youtube.com/watch?v=ydqReeTV_vk
I found this video today that seems similar to what you are talking about: https://youtu.be/M_vRgMBL0yA?si=5OsRiVnKt9A2Q4_u
Ok, I knew those genes were called something! Thinking about homeotic gene mutations has sufficiently jumbled my brain again though. (Hopefully, if I can code a simple analog to represent them, natural evolution can sort out any mess homeosis creates.)