A lot of projects start as a "small python file", but over time will grow into large and complex beasts - as they need to handle edge cases and complexities and requirements. Extrapolating that "programming is dead" based on anecdotal experiences from a hobby weekend project is very silly, and that's the joke.

Serializing an entire repository and feeding it to an LLM, and having the LLM change the code in response to specific asks, then storing the results - is not a trivial thing to implement. Think about large repositories with very long files, or repositories with a complex structure, or polyglot repositories. Projects where code and data are mixed together. Then think about security, with things like prompt injection in the source files, etc. Handling hallucinations.