main: keep only what reproduces the manuscript; everything else lives on dev

Removed from main (all preserved on the dev branch): the arXiv build and
its sources, design documents (blueprint, results summary, review responses,
essay drafts), tasks/ and CLAUDE.md, the cover letter and reference tooling,
two unused manuscript figures, and every experiment that feeds no figure or
number in the paper: the collapse null, the sexual-vs-asexual lineage, the
NK speciation variant, the 0.5B single-seed LLM prototypes, the compose and
society experiments with their calibration and pilot runs, and their
configs, runners, tests, figure scripts and PBS jobs. Their result bundles
are moved to results/_archive/ (ignored) so the parquets stay on disk.

Also: plot_llm_speciation reads the s{seed}/ layout; the mating-breadth
plot writes under its bundle name; Makefile targets reduced to the kept
experiments; REPRODUCING.md and README point to dev for the rest.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm

configs/inheritance/collapse_null.yaml

@@ -1,32 +0,0 @@
-experiment: E1_reproduce_collapse
-seed: 20260704
-n_replicates: 100
-generations: 600
-
-# Null model (blueprint 2.5-E1): no grounding, single teacher, no selection.
-# Starting from the truth makes the collapse narrative clean -- the tail is lost first,
-# support shrinks to 1, forward-KL diverges, and H decays geometrically at rate 1/n.
-# (The decay law E[H_t]=H_0(1-1/n)^t holds from any start; see the validation suite.)
-truth:
-  K: 500
-  R: 1
-  tail: zipf
-  zipf_s: 1.1
-  tail_frac: 0.5
-  tail_threshold: 1.0e-3
-  init: truth
-
-dynamics:
-  n: 100                 # distillation sample size = drift strength
-  teachers: {K_T: 1, rho: 0.0, q: 1.0}
-  grounding: {m: 0, policy: proportional}
-  selection: {mode: none, novelty_alpha: 0.0}
-  remint: {enabled: false, period: null, H_gate: null}
-
-metrics:
-  kl_floor: 1.0e-9
-  support_eps: 1.0e-9
-
-# No sweep: a single condition.
-output:
-  dir: results/collapse_null

configs/inheritance/sexual_vs_asexual_lineage.yaml

@@ -1,29 +0,0 @@
-experiment: E7
-kind: genotype_lineage
-seed: 20260705
-n_replicates: 20
-
-# (The advantage of sex — the dynamic mechanism behind E8): a single population adapts from all-wrong
-# toward a multi-locus optimum under selection + drift + mutation. Beneficial alleles arise in
-# different sub-lineages; recombination reassorts them into one genotype, while an asexual lineage
-# suffers clonal interference (the alleles compete and cannot combine). Expect the SEXUAL lineage
-# (recomb_rate=1) to climb toward the optimum faster than the ASEXUAL one (recomb_rate=0) — the
-# classical advantage of sex, and the reason a lone model lineage cannot do what a recombining
-# society can. Honest scope: a SPEED advantage, not a dramatic permanent gap (the single-population
-# ratchet is subtle); E8 carries the headline. Falsifier: sexual adapts no faster than asexual.
-
-genotype:
-  L: 12
-  n: 150           # population/resample size (drift strength)
-  mu: 0.02         # per-locus mutation (flip) rate
-  base: 1.3        # multiplicative selection: fitness weight = base^(#correct loci)
-  recomb_rate: 0.0 # overwritten per arm by the sweep
-  init: wrong      # start all-wrong (load L); adapt upward
-
-generations: 120
-
-sweep:
-  - param: genotype.recomb_rate
-    values: [0.0, 1.0]     # asexual vs sexual
-
-output: {dir: results/sexual_vs_asexual_lineage}

configs/inheritance/speciation_bdm_nk.yaml

@@ -1,22 +0,0 @@
-experiment: E12_nk
-kind: speciation
-seed: 12
-n_replicates: 15
-
-# E12 (NK variant) — the EPISTASIS WEDGE, the paper's distinct falsifiable claim: at matched divergence,
-# mergeability is governed by the EPISTASIS (ruggedness K) of the capability landscape, not by divergence
-# alone (every existing ML merge predictor is a divergence measure). Parents are LOCAL OPTIMA reached by
-# hill-climbing a Kauffman NK landscape from random starts; recombining them exposes broken co-adapted
-# blocks. As K rises, recombining two adapted parents flips from a gain (offspring above the worse parent)
-# to outbreeding depression (offspring below it). K=0 (additive) is the no-isolation control.
-
-speciation:
-  landscape: nk
-  L: 16
-  K: [0, 2, 4, 6, 8, 10]      # ruggedness / epistasis knob
-  n_pairs: 40                 # random parent-pairs (local optima) aggregated per landscape
-  recomb_rate: 0.5
-  n_offspring: 200
-
-output:
-  dir: results/speciation_bdm_nk