fix(bib): upsert merges tags/collections with stored row on URL dedupe (closes #624)

src/bib/store.py

@@ -219,9 +219,6 @@ class Store:
             ).fetchone()
             if existing:
                 ekey = existing["key"]
-                row = item.to_row()
-                row.pop("key", None)
-                # Merge tags
                 if tags:
                     for tag in tags:
                         label = tag.label if hasattr(tag, "label") else str(tag)
@@ -229,10 +226,19 @@ class Store:
                 if collection and collection not in item.collections:
                     item.collections.append(collection)
                 item.stamp_access()
+                # Merge with what's already stored — a re-ingest must
+                # never clobber tags/collections curated on the row
+                # since the last ingest (#624: the CY2027 NPRM lost its
+                # sup: registration tag to this and silently vanished
+                # from the tag-scoped Zotero sync). Deliberate removal
+                # goes through remove_tag, not upsert.
+                current = self.get(ekey)
                 row = item.to_row()
                 row.pop("key", None)
-                row["tags"] = item.tags
+                row["tags"] = list(dict.fromkeys([*current.tags, *item.tags]))
-                row["collections"] = item.collections
+                row["collections"] = list(
+                    dict.fromkeys([*current.collections, *item.collections])
+                )
                 self.update(ekey, **row)
                 return ekey
 

tests/bib/test_store.py

@@ -732,6 +732,38 @@ class TestUpsertDedup:
         assert "plain-tag" in got.tags
         s.close()
 
+    def test_upsert_preserves_curated_tags_on_existing(self) -> None:
+        """Regression #624: a re-ingest upsert must not clobber tags
+        added to the stored item since the last ingest (the CY2027 NPRM
+        lost sup:2027_PFS_NPRM this way and never reached Zotero)."""
+        s = Store(":memory:")
+        item1 = Rule(title="First", url="https://example.com/keep")
+        key = s.upsert(item1, tags=["source:federal-register"])
+        s.add_tag(key, "sup:2027_PFS_NPRM")  # curated after ingest
+
+        item2 = Rule(title="Re-ingested", url="https://example.com/keep")
+        item2.add_tag("source:federal-register")
+        key2 = s.upsert(item2)
+        assert key2 == key
+        got = s.get(key)
+        assert "sup:2027_PFS_NPRM" in got.tags
+        assert "source:federal-register" in got.tags
+        assert got.tags.count("source:federal-register") == 1
+        s.close()
+
+    def test_upsert_preserves_existing_collections(self) -> None:
+        """Regression #624: same wipe hazard via _sync_collections."""
+        s = Store(":memory:")
+        coll = s.ensure_collections({"Rules": {}})["Rules"]
+        item1 = Rule(title="First", url="https://example.com/keepc")
+        key = s.upsert(item1, collection=coll)
+
+        item2 = Rule(title="Re-ingested", url="https://example.com/keepc")
+        key2 = s.upsert(item2)
+        assert key2 == key
+        assert coll in s.get(key).collections
+        s.close()
+
 
 # ── _sync_collections with unknown key ─────────────────────────────