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/figS10_rugged_landscapes/README.md

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+# E9 — landscape robustness: when recombination helps, and the outbreeding-depression risk
+
+**Claim tested.** E8 showed sexual recombination assembling super-parent offspring — but on an
+*additive* landscape, where recombination trivially helps. The honest, credibility-critical question
+(the classic "why sex?" problem): does the benefit survive **epistasis**, or does merging entangled
+models break them?
+
+**Setup.** Parents are **local optima** ("trained models") of a **Kauffman NK landscape** (`L=12`),
+whose ruggedness `K` (epistatic interactions per locus) is swept together with the **recombination
+rate**. `K=0` is additive/smooth; larger `K` is rugged (co-adapted allele blocks, many local optima).
+Fitness ∈ [0,1]. 24 replicate landscapes; 200 offspring per point.
+
+### Symbols
+- **NK landscape** — tunable-ruggedness fitness landscape; `K` = epistasis (0 = additive, high = rugged).
+- **recombination rate** — per-gap crossover probability (0 = clonal / copy a parent; 0.5 = free recombination, loci independent).
+- **outbreeding depression** — offspring *less* fit than parents because recombination broke co-adapted allele blocks.
+
+### The two panels
+1. **The risk.** Mean offspring fitness *minus* best parent, vs recombination rate, one curve per
+   ruggedness `K`. On the additive landscape (`K=0`) it's flat at 0; as `K` grows the curves plunge
+   **negative**, and deeper the higher the recombination rate — **outbreeding depression, worse the
+   more entangled the skills and the more you mix** (`K=8`, free recombination: ≈ −0.23).
+2. **With selection, an optimal rate re-emerges.** Best-of-brood fitness (offspring selection) vs
+   rate per `K`, with parents dotted. On rugged landscapes a **nonzero intermediate recombination
+   rate** is best — enough mixing to find new combinations, not so much that it shatters good blocks.
+
+### Takeaway
+Recombination is not a free lunch. **Merge freely when skills are complementary/additive; merge
+sparingly — and always *select* offspring — when they are entangled.** This is the celebrated
+population-genetics result (recombination load / outbreeding depression) reproduced for AI model
+merging, and it turns the sexual metaphor from a lucky demo into a law with a design rule. The rescue
+— directed sex with offspring selection — is E10. **Falsifier (not triggered):** if recombination
+rate had no effect, or free recombination never underperformed the parents on rugged landscapes, the
+epistasis caveat would be moot.

results/figS10_rugged_landscapes/manifest.json

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+{
+  "experiment": "E9",
+  "master_seed": 20260705,
+  "git_commit": "62c68d6c8c4090e62cf9ee17ac7b7d1eff7a6955",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0"
+  },
+  "rows": 720,
+  "results_sha256": "73a737b333ee972ff1f878e18bf91b0aac58cb595c00c7b7fec3c18865971c4f"
+}

results/figS10_rugged_landscapes/resolved_config.yaml

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+experiment: E9
+seed: 20260705
+n_replicates: 24
+source_config:
+  experiment: E9
+  kind: recomb_landscape
+  seed: 20260705
+  n_replicates: 24
+  society:
+    L: 12
+    n_parents: 6
+    pop: 200
+  sweep:
+  - param: K
+    values:
+    - 0
+    - 2
+    - 4
+    - 6
+    - 8
+  - param: rate
+    values:
+    - 0.0
+    - 0.05
+    - 0.1
+    - 0.2
+    - 0.35
+    - 0.5
+  output:
+    dir: results/figS10_rugged_landscapes