I've wondered about this as well.

I don't have a complete answer, but so far documenting things as I go about doing them helps, especially if I write down what I tried, what went wrong, what worked and why. Its a lot while starting off, but over time as the concepts sink and become habits, my docs move to higher abstractions automatically and then it is mostly clear. The key words for me are 'train of thought'. The solution (the how) is important obviously, and always useful when quickly referring, but when making bigger changes it is more important to remember th why.

It is hella time consuming, needs dedication and practice and good tools (I couldn't start without org-mode myself)