We should have moved past storing code in files, using the filesystem as the symbol database of programs, a long time ago. There was a lot of interesting research toward this in Haskell, for example, but also Academia in general. There’d be lots of value in using things like SQLite for example, or just ecosystem-specific containers that know about the layout and can present it to an IDE or LLM or a runtime in whatever shape is best suited to the task.

for your point #2: people are trying out to give coding agents LSP support, not sure though how well it'll work but it gives coding agents a better idea of the language in which the code is written.