refactor: simplify workflow and remove obsolete code paths - #38
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…40) The deviation-penalty calibration drives its solves in-process, synthesizing a baseline and a main scenario per Broyden iteration, so the baseline named in `config/calibration/stability.yaml` is not a scenario the workflow declares. The stricter check introduced in #38 therefore rejected the config outright and `tools/calibrate stability` could not build its DAG.
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The feed, food_waste, food_demand and cost steps all read `deviation_penalty.yaml`, which the stability step writes at the end of the chain. The chain is a strict forward pass, so those four were fit against whatever vintage happened to be on disk, and `tools/calibrate --check` reported them stale after every complete run. None of them needs the file. feed, food_waste and food_demand pin production to actuals via `use_actual_production` and the enforced baselines, so the deviation penalty has nothing to act on; they now disable it. The cost step drives production stability through hard bounds, and the solve resolves the `"calibrated"` sentinel only for an enabled L1 penalty -- the input declaration in `calibration_artefact_inputs` now mirrors that gate instead of keying off the sentinel alone, which drops the dependency there without a config change. The dependency was inert: regenerating both tracked sets against the current model reproduces every artefact byte-identically, and `--check` now settles all-green after a full chain. Also re-stamps both sets after #36 and #38. Neither moved the artefacts -- verified by a full re-run, not by inspection.
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Summary
This is a multi-pass codebase cleanup focused on removing dead paths, consolidating duplicated logic, and making the active workflow easier to understand and maintain.
Overall, the branch changes 62 files and removes about 1,000 net lines.
Motivation
The repository had accumulated several one-off tools, transitional compatibility branches, duplicated execution adapters, and configuration options that were no longer consumed. Some scenario keys could also be accepted without affecting a solve, and several imported workflow modules were missing from Snakemake's code dependencies.
Keeping these paths made the supported workflow ambiguous and increased the chance of stale results or silently ignored configuration. Since GLADE is under active development and does not require backward compatibility, this PR makes the current interfaces explicit and fail-fast.
User impact
This intentionally removes obsolete command-line tools and configuration keys. Configurations must now be complete after merging with
config/default.yaml, and invalid scenario overrides fail instead of being ignored. User-visible removals and migration details are recorded underUnreleasedin the changelog.Validation
The full integration workflow was not executed because it would schedule retrieval rules requiring explicit network authorization. DAG construction and the existing local test coverage passed.