fix(setup): stop `enable --agent` from leaking local overrides into project settings

setupAgentHooksNonInteractive (the --agent entry point to entire enable) loaded the merged settings view and wrote it back wholesale to the target file, so local-only overrides (log_level, local_dev, ...) in settings.local.json still flattened into the shared settings.json on repos with a project settings file — the #1140 leak the previous fix closed for bare enable/disable, but not for this entry point.

Load settings scoped to the target file only (matching the pattern already used by updateStrategyOptions/updateGlobalSettings), and scope saveEnabledState's cross-file sync to just the "enabled" key instead of writing the full struct into the other scope's file.