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

results/E10/manifest.json

@@ -1,14 +0,0 @@
-{
-  "experiment": "E10",
-  "master_seed": 20260705,
-  "git_commit": "62c68d6c8c4090e62cf9ee17ac7b7d1eff7a6955",
-  "python": "3.14.5",
-  "libraries": {
-    "numpy": "2.5.0",
-    "scipy": "1.18.0",
-    "pandas": "3.0.3",
-    "pyarrow": "24.0.0"
-  },
-  "rows": 120,
-  "results_sha256": "b2d53d0a3949be0b67e3b8dffec56121d54e20c593e6302717a73a8a132f17cb"
-}