fix(index): dedupe ScanStats.pending by chunk_id

scan() extended stats.pending from each index_note() return and then again
from pending_embeds() (which re-reads every vec_pending=1 chunk in the db,
including the ones just indexed), so every freshly pending chunk was listed
twice and would be embedded twice.

Test: tests/test_index.py::test_scan_pending_has_no_duplicate_chunk_ids

src/mdmem/index.py

@@ -245,7 +245,14 @@ class Indexer:
         for note_id in set(known) - seen:
             self.remove(note_id)
             stats.removed += 1
-        stats.pending.extend(self.pending_embeds())
+        # pending_embeds() returns every vec_pending=1 chunk in the whole db,
+        # which includes the ones index_note() just appended above -- dedupe
+        # by chunk_id so each pending chunk is listed once, not twice.
+        seen_chunk_ids = {p.chunk_id for p in stats.pending}
+        for p in self.pending_embeds():
+            if p.chunk_id not in seen_chunk_ids:
+                seen_chunk_ids.add(p.chunk_id)
+                stats.pending.append(p)
         stats.seconds = time.monotonic() - started
         return stats
 

tests/test_index.py

@@ -209,6 +209,21 @@ def test_broken_yaml_is_skipped_not_fatal(idx):
     assert db.read().execute("SELECT count(*) FROM notes").fetchone()[0] == 1
 
 
+def test_scan_pending_has_no_duplicate_chunk_ids(idx):
+    """scan() extends ScanStats.pending from each index_note() return AND again
+    from pending_embeds(), so every pending chunk used to be listed twice."""
+    indexer, vault, db = idx
+    a = Note.new(title="A", body="body a", type="fact")
+    b = Note.new(title="B", body="body b", type="fact")
+    vault.write(a)
+    vault.write(b)
+    stats = indexer.scan()
+    assert stats.indexed == 2
+    chunk_ids = [p.chunk_id for p in stats.pending]
+    assert len(chunk_ids) == len(set(chunk_ids)), f"duplicate pending chunk ids: {chunk_ids}"
+    assert len(stats.pending) == 2
+
+
 def test_unchanged_embed_text_keeps_its_vector(idx):
     indexer, vault, db = idx
     n = Note.new(title="T", body="body", type="fact")