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Repository reorganization — 2026-06-10

The repo was reorganized for legibility and provenance. This file is the old → new path map. If a script breaks on a missing path, look it up here.

Policy: paper-render-critical paths were updated in place; the long tail of cluster/analysis scripts was not rewritten (they often assume a different cluster-side layout anyway). Fix those lazily — when you next touch a script, update its paths and delete its row here.

Directory moves

Old New Notes
gcp/ cluster/gcp/ compute helpers
sherlock/ cluster/sherlock/ compute helpers
glmer_ladder/ studies/glmer_ladder/ study code (self-contained)
input_estimation/ studies/input_estimation/ study code (self-contained)
cross_sectional_demographics/ studies/cross_sectional_demographics/ DONE (2026-06-11) — moved after the uncap refit landed
outputs/figs/ figs/ merged into the existing figs/; io/ merged
outputs/slides/ reports/slides/
outputs/marlowe/ reports/marlowe/ grant proposal
outputs/{model_explainer,chang_bergen_derivation,model_comparison_unified}.{tex,pdf} reports/ standalone docs
outputs/feng_eval/ fits/feng_eval/ LLM eval data
outputs/glmer_ladder/{sim_cache.rds,*.csv} fits/glmer_ladder/ study outputs
outputs/experiments.md journal/experiments.md canonical log
outputs/experiments_llms.md journal/experiments_llm.md LLM log (renamed)
outputs/PROVENANCE.md journal/PROVENANCE.md
outputs/_archive/ journal/archive/ old findings
outputs/*.md (notes/plans) journal/notes/
outputs/{param,input_rate,quality_variation}_table.*, predictors_alpha_zeta*.csv, etc. journal/results/ result tables
run_gamma_weekend.sh cluster/run_gamma_weekend.sh local-laptop fit launcher
outputs/ (deleted) fully dissolved

fits/, data/, model/, paper/, papers/ are unchanged. model/scripts/ remains the shared engine (the proc_dp / io_pooled / longitudinal / llm studies are indexed from studies/<name>/README.md, not moved).

Paths already fixed

  • paper/build_cache.R — outputs/glmer_ladder/sim_cache.rds → fits/…; input_estimation/… → studies/input_estimation/…
  • Makefile — outputs/figs → figs; outputs/model_explainer → reports/model_explainer
  • .gitignore — figs/feng_eval/manifest/quarto-artifact rules repointed

Known-stale references (fix when next touched)

  • cluster/sherlock/*.slurm, cluster/sherlock/glmer_ladder_submit.sh — invoke glmer_ladder/02_fit_one.R etc.; these run cluster-side under $HOME/standard_model_2 with a layout that may differ from this repo. Update glmer_ladder/ → studies/glmer_ladder/ if you re-sync the tree.
  • model/scripts/* — various scripts write to outputs/...; repoint to figs/, fits/, or journal/results/ as appropriate when you re-run them.
  • paper/_helpers.R — a comment references glmer_ladder/04b_plot.R (now studies/…).

Paper folder reorganization — 2026-08-15

After the acceleration paper moved to its own repo (~/Projects/acceleration), paper/ was reorganized around the input paper, now the only live manuscript here. Retired material went to paper/old/ (tracked history preserved via git mv; new render artifacts in old/ are gitignored).

Old New Notes
paper/input_paper/input_paper_text.qmd paper/input_paper.qmd the manuscript (renamed)
paper/input_paper/full_supplemental.qmd paper/full_supplemental.qmd SI; move fixes its relative figs/ refs
paper/input_paper/build_*.R paper/build_*.R 4 cache builders promoted
paper/standard_model_short.*, supplemental.qmd, science/, science.csl, science_template_v1.1/, build_cache_short.R, build_cache_si_{gamlss,settings}.R, _setup_shared.R, mockups/ paper/old/short_paper/ acceleration paper — canonical copies in ~/Projects/acceleration
si_clippings.qmd (repo root) paper/old/short_paper/ only copy — not in acceleration repo
paper/input_paper/standard_model.{qmd,pdf,tex,html}, supplemental.{pdf,tex}, PNAS .sty/.cls/.bst, paper/_extensions/, jabbrv*, widetext.sty, achemso.bst, acs-standard_model.bib paper/old/long_paper/ the original combined PNAS paper + format scaffolding
paper/Standard Model 2.0 BUCLD abstract.pdf paper/old/
paper/bucld/ (deleted) was empty

Path fixes made: input_paper.qmd bibliography ../standard_model.bib → standard_model.bib; build_cache.R header comment; .gitignore render rules repointed to input_paper* / full_supplemental* / old/. Render verified post-move (quarto render paper/input_paper.qmd → 10 pp PDF).