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Interestingly, modern "parsing" is more in the style you are looking for: You have MANY different views on the code, some of them "structural" to deal with it more efficiently for the specific domain.
I'm working in a spiritual successor for it, and found models like the relational/array are very friendly to a cohesive set of tools. But that is orthogonal to the use or not of files.
There’s an interesting project in the semantic diff/merge space that I have been keeping an eye out for https://github.com/afnanenayet/diffsitter