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

tests/test_mnist.py

@@ -14,7 +14,7 @@ import pytest
 
 pytest.importorskip("torchvision")
 
-from knowledge.metrics import forward_kl  # noqa: E402
+from inheritance.metrics import forward_kl  # noqa: E402
 from neural.config import MnistCfg, ModelCfg, OracleCfg  # noqa: E402
 from neural.mnist_data import (  # noqa: E402
     MnistSampler, assign_modes, fit_thickness_thresholds, make_mnist_truth, thickness_bin,