- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
(imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
where they feed none; configs keep their `experiment:` value so parquet
hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
SI Methods/tables updated; make clean no longer deletes tracked manifests;
reproduce.sh hashes the s{seed}/ layouts too
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
Clarity pass over the main text (36-item audit), Discussion rewrite and cut,
acknowledgements, Souly et al. as ref 62, lettered SI panels, model section
moved under Results; plus the untracked curriculum/society/compose/smol
configs, runners, figures, stats and tests that the SI already cites.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
Finishes the Layer 1 analytical core. All six experiments run with honest,
publication-quality figures; 71 tests green.
- E3 region-matched grounding: `grounding.exercised` knob + per-region tail
survival. Matched holds the exercised region's tail (0.49) where uniform
spreads thin and lets it collapse (0.07).
- E4 multi-teacher recombination: `run_coverage` runner. Union coverage matches
U(K_T,rho,q) exactly. Finding: mean-mixture distillation shows NO surviving
benefit (a conservation law — 1/K_T dilution cancels the union gain); a
union-preserving max-merge (M2N2-style) does. E4 reports both operators.
- E5 QD vs greedy: greedy drives fixation (H~0.01); QD holds H at 0.48-0.88,
rising with the novelty exponent.
- E6 re-mint gate: `arm` multi-override sweep. Re-minting a collapsed lineage
locks in divergence of KL-to-original; gating on diversity prevents it.
- E2 analysis add-ons (from the companion work order, numbers verified): new
analysis.py (reduce_to_stationary, critical_grounding with bootstrap CI ->
g*=0.048, 95% CI [0.047,0.050]); tail_band_metrics + per-band logging; the
E2 figure rebuilt as a 2x2 (defined g*+CI, g=0 flagged as a finite-time
artifact, tail item-vs-mass, per-rarity-band panel). Uses truth-mass-weighted
tail coverage rather than the raw (martingale) tail_mass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Scaffold plus the Layer 1 analytical core and the first two experiments.
- knowledge/: truth, metrics, teachers (2.7.1 shared-switch construction),
step, lineage, experiment, config, seeding (imported as `knowledge`).
- Validation spine green: neutral decay (Pred 1), fixation (Pred 2), exact
mutation-drift equilibrium (Pred 3), union coverage (Pred 5). 68 tests pass.
- E1 reproduces tail-first collapse. E2 delivers the headline: a grounding
phase boundary g* << 1, with stationary H tracking the exact H_eq closed
form (g=0.005 -> 68% of truth diversity; g=0.05 -> 96%).
- Reproducibility: uv venv from a hash-pinned uv.lock is the source of truth;
every run writes results.parquet + resolved_config.yaml + manifest.json
(lib versions, git commit, sha256). Figures and manifests tracked; the
large regenerable parquet is gitignored.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
