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

pyproject.toml

@@ -34,10 +34,10 @@ notebooks = ["jupyter>=1.0"]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
-# src-layout: src/knowledge/ is importable as `knowledge` (the normative package
-# name the scientific-validation conformance tests import). src/neural/ is Layer 1.5.
+# src-layout: src/inheritance/ (the inheritance model, importable as `inheritance`),
+# src/neural/ (trained networks) and src/llm/ (language models).
 [tool.hatch.build.targets.wheel]
-packages = ["src/knowledge", "src/neural", "src/llm"]
+packages = ["src/inheritance", "src/neural", "src/llm"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]