Restructure: descriptive tier and experiment names, paper/manuscript

- 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

results/E11/README.md

@@ -1,42 +0,0 @@
-# E11 — the dynamic Lamarckian society: the vertical claim (C3)
-
-**Claim tested.** The culmination. Everything before was a *single operator*; the society's
-load-bearing, un-preempted claim is that composing them makes **general capability climb over
-generations while specialties are re-earned**, and that **every operator is necessary** — remove one
-and it breaks. This is blueprint C3, the "vertical."
-
-**Setup.** A finite population of `N=60` agents (genotypes of `L=12` biallelic loci) evolves on a
-**rugged Kauffman NK landscape** (`K=8`) that *is* reality. Each generation composes: grounding,
-**directed recombination (sex)**, **quality-diversity selection**, and mutation. Grounding is made
-load-bearing by the **consensus-conformity (self-consumption)** mechanism — selection acts on
-`g·true_fitness + (1−g)·conformity`, where conformity = agreement with the population's own consensus,
-so at `g=0` the society optimises fitting-the-crowd rather than reality. A 4-arm ablation, 12
-replicate landscapes, 80 generations.
-
-### Symbols
-- **agent** = a model (a genotype); **reality** = the NK fitness landscape; **grounding `g`** = share of the selection signal that is real fitness vs conformity.
-- **directed sex** = recombine many parents + keep the fittest offspring (E10). **quality-diversity** = select for capability *and* novelty, so specialties persist.
-- **conformity − true fitness** = how far the population's mutual agreement exceeds its real capability (the self-consumption "delusion" signature).
-
-### The three panels (over generations)
-1. **The vertical climb.** Best real capability: the **full society (green) climbs to the global
-   optimum** (≈0.78 of 0.79), while **no_grounding (red) collapses** to a fit-looking but poor
-   consensus (0.48). `no_sex` and `no_diversity` plateau *below* the full society.
-2. **Specialties maintained.** Population diversity: the **full society explores longest** (diversity
-   decays slowly as it searches), while every ablation collapses diversity fast — `no_grounding`
-   almost immediately.
-3. **Self-consumption signature.** Conformity minus true fitness: **largest for `no_grounding`** — the
-   population strongly *agrees* while being *wrong*, the signature of training on its own consensus.
-
-### Takeaway — every operator is load-bearing
-- **full** → climbs to the optimum with diversity maintained. **The vertical claim.**
-- **no_grounding** → self-consumption collapse to an unfit consensus (train on the crowd → regress to a confident, wrong mean).
-- **no_sex** → can't recombine complementary specialists to escape local optima → plateaus below full.
-- **no_diversity (greedy)** → collapses diversity fastest, gets stuck at a *worse* local optimum.
-
-This integrates the whole study — E1–E6 (collapse/grounding/selection), the learning kernel, and
-E7–E10 (sexual transmission) — into one system, and shows the Lamarckian society needs **all** of
-grounding + directed sex + diversity to climb without collapsing. On a rugged landscape you need
-diversity to explore basins, sex to recombine them, and grounding to select on reality; remove any and
-you fail differently. **Falsifier (not triggered):** if any ablation had matched the full society, or
-the full society had failed to exceed every ablation, the integration claim would fail.