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/grounding/manifest.json

@@ -1,17 +0,0 @@
-{
-  "experiment": "grounding_phase_boundary",
-  "master_seed": 20260704,
-  "git_commit": "d22dd9d5355c4eb61a246ba9df1e57d5084d0dde",
-  "python": "3.14.5",
-  "libraries": {
-    "numpy": "2.5.0",
-    "scipy": "1.18.0",
-    "pandas": "3.0.3",
-    "pyarrow": "24.0.0",
-    "torch": "2.12.1"
-  },
-  "rows": 5022,
-  "results_sha256": "abfdd36ba4e5c42eb7540cc85e07236c5e291817c19cb96eda523bfc5178aed5",
-  "layer": "1.5",
-  "model_kind": "rnn"
-}