I agree with what you're saying, except the last part. Using ASTs as the source of truth (embedded in a source control forest) has benefits that are worth the difficulty.
What's the benefit? If your tooling already requires lossless round-trips to and from text, why invent a funky storage format that doesn't interoperate and can't be fixed with a text editor when it all blows up? You already have a perfect serialisation of the AST, in a format every other tool understands - that is, source code.
(And heaven forbid you should want to make a checkpoint commit that doesn't parse...)
- Using Merkle trees, we can assign every node a hash-based ID. So now we can refer to other nodes by ID. This lets us store a graph whose vertices are all the tree nodes.
- With the graph, we can now reference bindings not by string literal, but by ID. This eliminates shadowing problems and missing imports.
- There is now one source of truth for the names of variables and functions. As a result, in source control, a commit that renames something is a one-line change.
