For the last few months though I've been thinking a lot about what you said at the end there. What if version control actually understood the code it was tracking, not as lines of text but as the actual structures we write and think in, functions, classes, methods, the real building blocks? A rename happening on one branch and an unrelated function addition on another aren't a real conflict in any meaningful sense, they only look like one because every tool we have today treats source code as flat text files.
For enhancing this kind of structural intelligence I started working on https://github.com/ataraxy-labs/sem, which uses tree-sitter to parse code into semantic entities and operates at that level instead of lines. When you start thinking of code not as text there's another dimension where things can go, even a lot of logic at the comiler level with call graphs becomes useful.
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