CLI migration

Legacy command or option Replacement
mudidi run --benchmark ... mudidi benchmark run --config benchmark.yaml
Shell model/ablation matrices mudidi benchmark sweep --config sweep.yaml
mudidi eval stage1 ... mudidi benchmark evaluate stage1 --config evaluation.yaml
mudidi eval stage2 ... mudidi benchmark evaluate stage2 --config evaluation.yaml
mudidi-eval-flat mudidi benchmark evaluate stage1
mudidi-eval-stage2-mdf mudidi benchmark evaluate stage2
Agentic flags mudidi run --stage1-agentic / --stage2-agentic and related options, or typed YAML
Advanced pipeline/cache/VLM settings Typed YAML sections
--stage1-mode column pipeline.stage1_mode: column
--parse-rules-file PATH pipeline.parse_rules_file: PATH
--toolbox-pdf PATH input.toolbox_pdf: PATH
--stage1-source predictions pipeline.stage1_source: predictions

The command syntax changes deliberately; experiment names, models, stage choices, input sources, and output layouts remain reproducible through canonical YAML.