[PaulRegular]

Plotting code is grouped by purpose, residual plots offer Standardized/OSA without bubble outlines, and the opening Model structure page uses responsive HTML/SVG with Diagram and Function calls tabs. Explicit hover vectors stay aligned with model frames and partial residual data.

Comparative analyses now use a manually refreshed, ignored SAIO snapshot selected by a tracked commit manifest. The five CSVs are retained and parsed once into an RDS cache. Fitting, dashboard rendering/indexing and overview figures are separate; the caller chooses the future plan, and workers receive stock-specific inputs. Operational scripts and all 115 recipes are flattened under scripts/. Eleven missed F-covariate locations are corrected without changing formulas or fitting controls.

Retires check_obs()/tidy_mat() aliases, dead implementations and old saved-fit migrations. Shared fixtures remove nine repeated fits and two duplicate dashboard renders. Documentation is consolidated and the cheatsheet/companion dashboard regenerated through their provenance-aware generator. Model equations, M boundary conventions, assessment hypotheses, existing cached fits and canonical exports are preserved. Version remains 0.1.1.9001.

Validation:

• R CMD check --no-manual: Status OK; 4,683 assertions, zero failures/warnings/skips. Final packaged code is identical to the checked source.
• 135/137 comparative scripts pass. Remaining failures: a direct reduced-age fit returns false convergence/non-positive-definite covariance, and Rockall haddock has duplicate weight rows. Neither was tuned or suppressed.
• Preliminary preparation, fitting disabled: 65 prepared, 14 declared source blocks, 1 Rockall duplicate-weight failure.
• Caller-plan equivalence, subprocess returns, timeouts/checkpoints, snapshot refresh and troubleshooting dashboards pass.
• Responsive diagram geometry/model switching checked at 1200/700/400 px; both PDF pages inspected. Website reference/home build passes locally.
• All 20 primary canonical exports/figures retain their previous SHA-256 hashes.

The regenerated example retains one unsuccessful SAM hindcast fold and the warning about unequal validation coverage. This PR remains a draft; no merge or release is included.