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/pnas/main.tex

@@ -1,27 +0,0 @@
-% Manuscript draft — readable single-column build for review/iteration (tectonic/XeLaTeX). Content is
-% generated from main.md by build.py; journal-template reflow happens at submission.
-\ifdefined\XeTeXversion\else\ifdefined\pdfoutput\pdfoutput=1\fi\fi
-\documentclass[11pt]{article}
-
-\usepackage[a4paper, margin=1.0in]{geometry}
-\usepackage{graphicx}
-\usepackage{amsmath, amssymb}
-\usepackage[hidelinks]{hyperref}
-\usepackage{microtype}
-
-\setlength{\parskip}{0.35em}
-
-\title{\textbf{The evolution of sex for artificial intelligence}\\[0.5em]
-\large A population-genetic framework for multigenerational model populations}
-\author{Giorgio F.\ Gilestro\\[0.2em]
-\normalsize Department of Life Sciences, Imperial College London\\
-\normalsize \href{mailto:giorgio@gilest.ro}{giorgio@gilest.ro} \,\(\cdot\)\,
-\href{https://lab.gilest.ro}{lab.gilest.ro}}
-\date{Draft}
-
-\begin{document}
-\maketitle
-
-\input{body}
-
-\end{document}