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/arxiv/md2tex.py

@@ -19,11 +19,11 @@ OUT = Path(__file__).resolve().parent / "body.tex"
 
 # Figure references in the text -> (graphics file under figs/, caption).
 FIGURES = {
-    "results/E14/E14.png": ("figs/E14.pdf",
+    "results/figS13_mating_breadth/E14.png": ("figs/E14.pdf",
         "Mating systems (E14): the best mate-pool breadth shrinks as skills get more entangled. "
         "(A) best fitness peaks at intermediate breadth on rugged landscapes; (B) the population mean "
         "is monotonically favoured by promiscuity; (C) diversity is monotonically destroyed by it."),
-    "results/E12/E12.png": ("figs/E12.pdf",
+    "results/fig5_speciation_bdm/E12.png": ("figs/E12.pdf",
         "Model speciation, analytic (E12): hybrid fitness vs divergence traces compatible $\\rightarrow$ "
         "outbreeding depression $\\rightarrow$ inviability; the isolation cliff arrives earlier the "
         "denser the incompatibilities (epistasis), and damage grows super-linearly (the Orr--Turelli "