fix(bib): keep unmodeled extra_json keys on an updating upsert

upsert merged incoming extra_json into current.to_row(), which only
serializes the keys the item model declares. Any upsert that changed a
row erased the rest: the tagger's llm_tags state (forcing a re-judge),
a rule's federal_register_citation. Merge against the stored JSON and
compare dicts, so those keys survive and alone never dirty a row.

src/bib/store.py

@@ -324,14 +324,23 @@ class Store:
         # every time, so a column-wise empty check can't apply — merge
         # the decoded dict per key instead: a stored key survives unless
         # the incoming payload sets it to a non-empty value.
-        cur_extra = json.loads(cur_row.get("extra_json") or "{}")
+        # Read the stored JSON itself, not current.to_row(): the model
+        # drops keys it does not declare (the tagger's llm_tags state, a
+        # rule's federal_register_citation), and rebuilding from it would
+        # erase them on any updating upsert.
+        stored_raw = con.execute(
+            "SELECT extra_json FROM items WHERE key = ?", (ekey,)
+        ).fetchone()[0]
+        cur_extra = json.loads(stored_raw or "{}")
         new_extra = json.loads(new_row.get("extra_json") or "{}")
         merged_extra = {**cur_extra, **{k: v for k, v in new_extra.items() if v}}
         merged_extra_json = json.dumps(merged_extra)
         new_row["extra_json"] = merged_extra_json
 
-        same_cols = all(
-            new_row.get(c, "") == cur_row.get(c, "") for c in self._COMPARE_COLS
+        same_cols = merged_extra == cur_extra and all(
+            new_row.get(c, "") == cur_row.get(c, "")
+            for c in self._COMPARE_COLS
+            if c != "extra_json"
         )
         if (
             same_cols

tests/bib/test_store_upsert_noop.py

@@ -143,3 +143,29 @@ def test_non_empty_incoming_extra_json_key_updates_that_key_only():
     # ...but the blank incoming effective_date did not blank the stored one.
     assert stored.effective_date == "2026-01-01"
     assert stored.cms_id == "CMS-1848-P"
+
+
+def test_unmodeled_extra_json_key_survives_an_updating_upsert():
+    """Keys the item model does not declare (the tagger's llm_tags state,
+    a rule's federal_register_citation) live only in the stored JSON. An
+    upsert that changes the row must carry them over, not rebuild the
+    stored side from the model and drop them."""
+    import json
+
+    s = _store()
+    key, _ = s.upsert_status(_item(abstract="body"))
+    s.merge_extra(key, {"llm_tags": {"version": 2, "tags": {"telehealth": {}}}})
+    _, status = s.upsert_status(_item(abstract="body, enriched"))
+    assert status == "updated"
+    row = (
+        s._con().execute("SELECT extra_json FROM items WHERE key=?", (key,)).fetchone()
+    )
+    assert json.loads(row[0])["llm_tags"]["version"] == 2
+
+
+def test_unmodeled_extra_json_key_alone_does_not_make_upsert_dirty():
+    s = _store()
+    key, _ = s.upsert_status(_item())
+    s.merge_extra(key, {"llm_tags": {"version": 2}})
+    _, status = s.upsert_status(_item())
+    assert status == "unchanged"