Function layered_config 

pub fn layered_config(cli: Vec<String>, file_config: RawConfig) -> RawConfig

Layer CLI flags over the environment over the agent’s settings file.

Returns the merged-but-UNRESOLVED inputs. Validation is deliberately not done here: serve must start even when the result cannot resolve, so resolution happens once inside ServerState and its failure is reported on the first tool call rather than at startup.

A CLI flag that was silently ignored would be a config trap, so flags DO layer over the environment rather than being an either/or — and the settings file sits below both, so a user can override a committed project setting for one session without editing it.