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

paper/response-to-review-3.md

@@ -1,7 +1,7 @@
 # Response to the third review (of the PNAS-format draft)
 
 *All five priority fixes are made, plus the presentation items. The revised draft is
-`paper/pnas/main.md` (rebuilt PDF alongside); the long-form document and the results documentation
+`paper/manuscript/main.md` (rebuilt PDF alongside); the long-form document and the results documentation
 were corrected wherever they carried the same overstatements. Point-by-point:*
 
 ## 1. The averaging proposition (your §2) — you are right, and the text now proves what it claims