docs: fix two doc/code contradictions (audit D-2, D-4)

- D-2 config.py: graph_cite_boost_alpha described the OLD inverted formula
  (score = dense * (1 + alpha*pr)); the code divides distance. Document the
  actual boosted_distance = distance / (1 + alpha*pr).
- D-4 synthesis.py: write_leads claimed an 'append-only' INDEX.md that keeps
  previously-recorded ids; _update_index actually rebuilds from on-disk glob.
  Docstring now matches the implementation.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

codex/config.py

@@ -295,7 +295,8 @@ class Settings(BaseSettings):
         le=1.0,
         description=(
             "Weight of the PageRank citation-boost in hybrid search. "
-            "Final score = dense_score * (1 + alpha * pagerank_score). "
+            "boosted_distance = distance / (1 + alpha * pagerank_score) — dividing "
+            "lowers the cosine distance of high-PageRank papers (lower = closer). "
             "Set to 0.0 to disable the boost without removing the flag."
         ),
     )

codex/synthesis.py

@@ -773,10 +773,11 @@ def write_leads(leads: list[Lead], leads_dir: str) -> None:
     * Grounded leads → ``leads_dir/grounded/<id>.md``
     * Conjectures   → ``leads_dir/conjectures/<id>.md`` (HARD invariant)
 
-    The function ALSO maintains an append-only ``leads_dir/INDEX.md``:
-    a previously-recorded id is kept on subsequent runs even if it is
-    overwritten with a newer body. The two sections (grounded /
-    conjectures) are visibly separated.
+    The function ALSO rebuilds ``leads_dir/INDEX.md`` from the on-disk files on
+    every run (see :func:`_update_index`): it reflects whatever lead files
+    currently exist under ``grounded/`` and ``conjectures/``, listed as two
+    visibly separated sections. It is not append-only — a deleted lead file
+    drops out of the index on the next run.
 
     Notes
     -----