SI: adopt the clearer rewrite, with factual corrections; fix two build bugs it exposed

Prose: adopted the simplified rewrite for the Reproducibility preamble, SI
Text S1 and S2, and the two tables. It reads better - shorter sentences, no
shouty caps, no self-commentary in the proposition headings.

Fact-checked against the artifacts before adopting. Corrections:
- Table S2 said grounding retention used "18+ replicates per point". E2 uses
  100 lineages; 18 is the *neural* grounding sweep. (Pre-existing error,
  faithfully carried over by the rewrite.)
- The emergent parents' 0.535/0.474 are the accuracies at the LONGEST
  divergence (t_div=3200), not overall means (0.595/0.545); now qualified.
  Verified merge holds 0.954-0.956 at every divergence, residual exactly
  0.000 in both emergent conditions.
- Dropped an invented run date (2026-08-11; the run is from 2026-09-06) and
  an internal project-phase reference ("Phase 3").
- The llm_speciation duration question is no longer open - it ran, and found
  no isolation from over-training (1-12 epochs); text updated.
- Restored the confidence-weighting numbers the rewrite dropped: paired
  bootstrap contrast |rho| = -0.021, CI [-0.130, +0.059] (re-derived), plus
  the nuance that the weighting does sharpen the level contrast.
- "Minimal model" -> "biological model"; "LLM tier in progress" -> done.
- Trimmed an unverifiable citation ("neuron-identifiability approaches...")
  to the reference the bibliography actually carries.

Two rendering bugs the LaTeX version exposed, both pre-existing:
- Greek and several math symbols were absent from build.py's unicode map, so
  alpha and epsilon were rendering as missing-glyph boxes in the SI. Added
  Greek, set membership, superscripts, proper minus. Both PDFs now contain
  zero missing glyphs.
- inline() split on code spans BEFORE applying emphasis, so any italic
  containing `code` was torn into fragments - visible in the main text as a
  literal "is*" and mis-scoped italics on p. 3. Code spans are now stashed
  behind sentinels first. This fixed the manuscript, not just the SI.
- A leading markdown H1 leaked into the body as literal text; the wrapper
  supplies the title, so it is now skipped.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v

paper/pnas/build.py

@@ -106,9 +106,17 @@ FIGURES: dict[str, tuple[list[str], str]] = {
         "between predictors are not individually significant."),
 }
 
-UNICODE = {"—": "---", "–": "--", "→": r"\(\rightarrow\)", "≈": r"\(\approx\)", "≥": r"\(\geq\)",
-           "≳": r"\(\gtrsim\)", "×": r"\(\times\)", "·": r"\(\cdot\)", "μ": r"\(\mu\)",
-           "ρ": r"\(\rho\)", "≤": r"\(\leq\)", "≪": r"\(\ll\)", "∝": r"\(\propto\)"}
+UNICODE = {
+    # Multi-character sequences first: esc() applies these in insertion order.
+    "⁽ᵏ⁾": r"\(^{(k)}\)", "⁻³": r"\(^{-3}\)", "⁻⁴": r"\(^{-4}\)",
+    "—": "---", "–": "--", "→": r"\(\rightarrow\)", "≈": r"\(\approx\)", "≥": r"\(\geq\)",
+    "≳": r"\(\gtrsim\)", "×": r"\(\times\)", "·": r"\(\cdot\)", "μ": r"\(\mu\)",
+    "ρ": r"\(\rho\)", "≤": r"\(\leq\)", "≪": r"\(\ll\)", "∝": r"\(\propto\)",
+    # Greek and math symbols: the typewriter font has no Greek, so these must become math.
+    "α": r"\(\alpha\)", "β": r"\(\beta\)", "ε": r"\(\varepsilon\)", "Δ": r"\(\Delta\)",
+    "Σ": r"\(\Sigma\)", "∈": r"\(\in\)", "≠": r"\(\neq\)", "±": r"\(\pm\)",
+    "∼": r"\(\sim\)", "−": r"\(-\)", "²": r"\(^{2}\)", "³": r"\(^{3}\)", "⁴": r"\(^{4}\)",
+}
 SPECIALS = {"&": r"\&", "%": r"\%", "#": r"\#", "_": r"\_", "$": r"\$",
             "~": r"\textasciitilde{}", "^": r"\textasciicircum{}"}
 
@@ -123,19 +131,21 @@ def esc(s: str) -> str:
 
 
 def inline(s: str) -> str:
-    parts = re.split(r"(`[^`]*`)", s)
-    out = []
-    for p in parts:
-        if p.startswith("`") and p.endswith("`") and len(p) >= 2:
-            out.append(r"\texttt{" + esc(p[1:-1]) + "}")
-        else:
-            p = esc(p)
-            p = re.sub(r"\[([^\]]+)\]\((https?://[^)]+)\)", r"\\href{\2}{\1}", p)
-            p = re.sub(r"\*\*([^*]+)\*\*", r"\\textbf{\1}", p)
-            p = re.sub(r"\*([^*]+)\*", r"\\emph{\1}", p)
-            p = re.sub(r'"([^"]+)"', r"``\1''", p)
-            out.append(p)
-    return "".join(out)
+    # Code spans are stashed behind sentinels *before* emphasis is applied, so that an italic or
+    # bold span containing `code` is still matched as one span (splitting first would break it).
+    codes: list[str] = []
+
+    def stash(m: re.Match) -> str:
+        codes.append(r"\texttt{" + esc(m.group(0)[1:-1]) + "}")
+        return f"\x00{len(codes) - 1}\x00"
+
+    s = re.sub(r"`[^`]*`", stash, s)
+    s = esc(s)
+    s = re.sub(r"\[([^\]]+)\]\((https?://[^)]+)\)", r"\\href{\2}{\1}", s)
+    s = re.sub(r"\*\*([^*]+)\*\*", r"\\textbf{\1}", s)
+    s = re.sub(r"\*([^*]+)\*", r"\\emph{\1}", s)
+    s = re.sub(r'"([^"]+)"', r"``\1''", s)
+    return re.sub(r"\x00(\d+)\x00", lambda m: codes[int(m.group(1))], s)
 
 
 def figure_env(name: str) -> str:
@@ -192,6 +202,8 @@ def convert(text: str) -> str:
             emit_table(block, out)
         elif first == "---" and len(block) == 1:
             out.append("\\medskip\\hrule\\medskip"); out.append("")
+        elif first.startswith("# ") and not first.startswith("## "):
+            continue                                       # document title: the wrapper supplies it
         elif first.startswith("## "):
             out.append(f"\\section*{{{inline(first[3:])}}}"); out.append("")
         elif first.startswith("### "):