Reproducibility pass: figure map, one-command reproduce.sh, notebooks, Makefile gaps

An audit of the figure pipeline found real sync gaps, now closed:

- `paper/pnas/make_figs.py` (which draws every manuscript figure) was invoked
  by NO Makefile target or script - a manual step. Added `make paper-figures`.
- `configs/llm/epistasis{,_compat}.yaml` were reachable from nothing at all,
  despite producing Fig. 3C-D. Added `make llm-epistasis` (+ its statistics).
- `make figures` never regenerated the MNIST montage that Fig. 2B embeds;
  it now runs with the `mnist` target (it needs torch - it re-simulates).
- Added `make llm-society`, `env-notebooks`, `notebooks`.

New REPRODUCING.md is the authoritative map: every manuscript panel -> the
artifact it plots -> the config that produced it -> that config's seed, plus
the determinism policy (biological tier bitwise; GPU tiers statistical), the
seed-provenance statement, and an artifact-hash verification snippet. All 44
committed bundles currently hash-match their manifests, and figure
regeneration is pixel-identical (verified by comparison).

reproduce.sh delivers the one-command reproduction the paper's Methods
promises, writing REPRODUCED.md with recomputed hashes per bundle.

Two executed notebooks: 01 builds the Wright-Fisher model from scratch and
checks both closed forms interactively (runs in ~1 min on a laptop); 02
verifies artifact hashes then regenerates and displays all seven manuscript
figures. Both execute end-to-end (`make notebooks`).

Also pins `.python-version` to 3.14: the interpreter was previously
unpinned, and a `uv sync` silently switched it to 3.11 mid-session (see
tasks/lessons.md). README rewritten - it still described a Layer-1-only repo
of E1-E6 and pointed at a figure_manifest.md that does not exist.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v

reproduce.sh

@@ -0,0 +1,82 @@
+#!/usr/bin/env bash
+# One-command reproduction of the paper's biological-model tier (see REPRODUCING.md).
+#
+#   ./reproduce.sh              env -> tests -> biological model at committed seeds -> figures
+#   ./reproduce.sh --with-gpu   also runs the trained-network, MNIST, and language-model tiers
+#
+# Writes REPRODUCED.md: every artifact's recomputed content hash next to the committed one, so a
+# reader can see at a glance which bundles reproduced bitwise. The biological-model tier must match
+# exactly; GPU tiers are statistically reproducible only (REPRODUCING.md section 5).
+set -euo pipefail
+
+WITH_GPU=0
+[[ "${1:-}" == "--with-gpu" ]] && WITH_GPU=1
+
+cd "$(dirname "$0")"
+START=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
+say() { printf '\n\033[1m== %s\033[0m\n' "$1"; }
+
+say "Environment (uv sync from the committed uv.lock)"
+if ! command -v uv >/dev/null; then
+  echo "uv not found. Install it: curl -LsSf https://astral.sh/uv/install.sh | sh" >&2
+  exit 1
+fi
+if [[ $WITH_GPU -eq 1 ]]; then
+  uv sync --extra dev --extra neural --extra mnist --extra llm
+else
+  uv sync --extra dev
+fi
+
+say "Tests (correctness + closed-form scientific validation)"
+uv run pytest -q
+
+say "Biological-model tier at the committed seeds"
+make layer1
+
+if [[ $WITH_GPU -eq 1 ]]; then
+  say "Trained-network tier"; make neural
+  say "Real-MNIST tier";      make mnist
+  say "Language-model tier";  make llm
+  say "LLM predictive test";  make llm-epistasis
+fi
+
+say "Figures (pure functions of the artifacts)"
+make figures
+make paper-figures
+
+say "Hash report -> REPRODUCED.md"
+uv run python - "$START" "$WITH_GPU" <<'EOF'
+import hashlib, json, pathlib, subprocess, sys, datetime
+
+start, with_gpu = sys.argv[1], sys.argv[2] == "1"
+commit = subprocess.run(["git", "rev-parse", "HEAD"], capture_output=True, text=True).stdout.strip()
+rows, exact, differ, missing = [], 0, 0, 0
+for man_path in sorted(pathlib.Path("results").glob("*/manifest.json")):
+    man = json.loads(man_path.read_text())
+    pq = man_path.parent / "results.parquet"
+    want = man.get("results_sha256", "")
+    if not pq.exists():
+        status, got, missing = "not run", "-", missing + 1
+    else:
+        got = hashlib.sha256(pq.read_bytes()).hexdigest()
+        if got == want:
+            status, exact = "bitwise match", exact + 1
+        else:
+            status, differ = "differs", differ + 1
+    rows.append((man_path.parent.name, man.get("master_seed", "-"), status, want[:12], got[:12]))
+
+out = [
+    "# Reproduction report", "",
+    f"- Started: {start}", f"- Finished: {datetime.datetime.now(datetime.UTC):%Y-%m-%dT%H:%M:%SZ}",
+    f"- Commit: `{commit}`", f"- GPU tiers included: {'yes' if with_gpu else 'no'}",
+    f"- Bundles: {exact} bitwise match, {differ} differ, {missing} not run", "",
+    "The biological-model tier is bitwise reproducible and must show `bitwise match`. GPU tiers are",
+    "statistically reproducible only, so `differs` is expected there (see REPRODUCING.md section 5).",
+    "", "| Bundle | Seed | Status | Committed sha256 | Recomputed |", "|---|---|---|---|---|",
+]
+out += [f"| `{n}` | {s} | {st} | `{w}…` | `{g}…` |" for n, s, st, w, g in rows]
+pathlib.Path("REPRODUCED.md").write_text("\n".join(out) + "\n")
+print(f"{exact} bitwise match, {differ} differ, {missing} not run -> REPRODUCED.md")
+EOF
+
+say "Done. See REPRODUCED.md, and REPRODUCING.md for the figure-by-figure map."