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/fig4_society_ablation/README.md

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+# 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.

results/fig4_society_ablation/manifest.json

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+{
+  "experiment": "E11",
+  "master_seed": 20260705,
+  "git_commit": "48181a1c846f41e9254abe4b1d0f843d1df9667f",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0"
+  },
+  "rows": 3888,
+  "results_sha256": "e8d2c3ecb5200578d16a977d147b6ee05ebf83e1a81d9287f6a740114ef3968a"
+}

results/fig4_society_ablation/resolved_config.yaml

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+experiment: E11
+seed: 20260705
+n_replicates: 12
+source_config:
+  experiment: E11
+  kind: dynamic_society
+  seed: 20260705
+  n_replicates: 12
+  society:
+    L: 12
+    K: 8
+    N: 60
+    g: 0.85
+    mu: 0.03
+    novelty: 0.5
+    n_off: 120
+    recomb_rate: 0.2
+    sex: true
+    select: qd
+  generations: 80
+  sweep:
+  - param: arm
+    values:
+    - name: full
+      set: {}
+    - name: no_grounding
+      set:
+        society.g: 0.0
+    - name: no_sex
+      set:
+        society.sex: false
+    - name: no_diversity
+      set:
+        society.select: greedy
+        society.novelty: 0.0
+  output:
+    dir: results/fig4_society_ablation