Save generated run inputs as RunInputFile records

[bnmajor]

Generated YAML has to exist as real files for CODES, as well as artifacts in the database.

CODES resolves all five paths (topology_yaml_file, traffic_trace_file, and the three log paths) with configuration_get_value_relpath, relative to the config file - not the working directory. And logs/ must exist before launch or the run aborts at startup. There is no stdin and no CLI override, so handing config to the binary from the DB is not an option.

• RunInputFile: FK to Run, S3FileField, and a kind field (topology_yaml/config_yaml/traffic_trace).
• At launch, build the per-run directory: config, topology, trace (if any), and a pre-created logs/ subdirectory.
• Generate both YAMLs into that directory, then attach them as RunInputFile records.