fix(state): add REINDEX strategy to repair stale B-tree indexes (#63386)

When PRAGMA integrity_check reports 'wrong # of entries in index' for
B-tree indexes (e.g. idx_sessions_handoff_state), the existing repair
strategies (FTS rebuild, sqlite_master dedup, drop-FTS+VACUUM) don't
address the mismatch. Add Strategy 0.5: run REINDEX to rewrite the
index b-tree from canonical table rows before escalating to more
destructive strategies.

hermes_state.py

@@ -748,6 +748,29 @@ def repair_state_db_schema(db_path: Path, *, backup: bool = True) -> Dict[str, A
     except sqlite3.DatabaseError as exc:
         logger.warning("state.db FTS in-place rebuild pass failed: %s", exc)
 
+    # ── Strategy 0.5: rebuild stale B-tree indexes (#63386) ──
+    # PRAGMA integrity_check can report "wrong # of entries in index" when a
+    # B-tree index (e.g. idx_sessions_handoff_state) falls out of sync with its
+    # base table. REINDEX rewrites the index b-tree from the canonical table
+    # rows using the existing index definition, fixing the mismatch without
+    # touching data or FTS schema.
+    try:
+        conn = sqlite3.connect(str(db_path), isolation_level=None)
+        try:
+            conn.execute("REINDEX")
+            conn.commit()
+        finally:
+            conn.close()
+        if _db_opens_cleanly(db_path) is None:
+            report["repaired"] = True
+            report["strategy"] = "reindex_btree"
+            logger.warning(
+                "state.db B-tree indexes rebuilt via REINDEX: %s", db_path
+            )
+            return report
+    except sqlite3.DatabaseError as exc:
+        logger.warning("state.db REINDEX pass failed: %s", exc)
+
     # ── Strategy 1: de-duplicate sqlite_master (keeps FTS index) ──
     try:
         conn = sqlite3.connect(str(db_path), isolation_level=None)

tests/test_state_db_malformed_repair.py

@@ -487,6 +487,35 @@ def test_repair_noop_db_uses_already_healthy_shortcut(tmp_path):
     assert report["strategy"] == "already_healthy"
 
 
+def test_repair_rebuilds_stale_btree_indexes(tmp_path, monkeypatch):
+    """repair_state_db_schema uses REINDEX for 'wrong # of entries in index'.
+
+    When PRAGMA integrity_check reports a stale B-tree index (e.g.
+    idx_sessions_handoff_state), the FTS-rebuild and dedup strategies don't
+    help — REINDEX rewrites the index b-tree from the canonical table rows.
+    """
+    db_path = tmp_path / "state.db"
+    _build_healthy_db(db_path)
+
+    _reason = "wrong # of entries in index idx_sessions_handoff_state"
+    _call_count = {"n": 0}
+    _real_check = hermes_state._db_opens_cleanly
+
+    def _simulated_check(path):
+        _call_count["n"] += 1
+        # initial health check + post-Strategy-0 check report corruption;
+        # after REINDEX (Strategy 0.5) the DB is healthy.
+        if _call_count["n"] <= 2:
+            return _reason
+        return _real_check(path)
+
+    monkeypatch.setattr(hermes_state, "_db_opens_cleanly", _simulated_check)
+
+    report = repair_state_db_schema(db_path)
+    assert report["repaired"] is True
+    assert report["strategy"] == "reindex_btree"
+
+
 def test_select_cached_agent_history_prefers_longer_live_transcript():
     """Gateway guard keeps the live transcript when persisted history lags."""
     from gateway.run import _select_cached_agent_history