It seems like a common intuition in software is the "code smell", where you can just look at some code and tell if it will be "maintainable" or "good", for some value of that.

I've come to think of it more as a "familiarity" though - where if you're familiar with writing stable and maintainable systems, you'll get the right smells - but some people have opposite feelings about systems, and it seems like they are people that have the opposite type of experience as well.

Other types of intuition I think are based mostly on pattern recognition. If you have a system that makes a set of choices that follows a well known pattern to you, your brain can start predicting what has been done where, and with enough confirmation, can start feeling confident about the behavior of other parts not yet scrutinized. Once again, if things are done in an unfamiliar way, all that evaporates and one needs to fall back to looking at the low level strategies and techniques.

I think there are two separate issues here. One is 'just' another way of understanding or visualizing a concept or process: "look the problem over and see if you can understand the way it behaves, roughly, when you change some of the numbers". Isn't this exactly what you do with a debugger when you step through the code? Or if I'm designing a data structure or algorithm, I have to play around in my head, or with pen and paper, before even thinking about going near a keyboard.

The other issue is 'allowing' oneself to imagine and visualize these things (math/physics equations / software). I don't think the point is to restrict yourself to things for which you have physical intuition, it's more that it's easier to go from physical experience -> intuition about physics phenomena that are closely related to physical experience -> intuition about math /physics /software that don't have a counterpart in our physical experience as humans e.g. quantum mechanics

As hard as the actual calculations may be, the main feature of a mechanics is that it is conceptually simple.

Now, software just isn't. Managing complexity requires a completely different intuition from exploring a simple space.

That's what this is about: http://worrydream.com/SeeingSpaces/