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

reproduce.sh

@@ -31,7 +31,7 @@ say "Tests (correctness + closed-form scientific validation)"
 uv run pytest -q
 
 say "Biological-model tier at the committed seeds"
-make layer1
+make inheritance
 
 if [[ $WITH_GPU -eq 1 ]]; then
   say "Trained-network tier"; make neural
@@ -51,7 +51,7 @@ 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")):
+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", "")