fix(graphrag): review fixes — replay-safe writes, strict count, zero weights

Three findings from review, all on code this branch introduced.

apply_chunk was not replay-safe. commit() can report connection loss *after*
Postgres committed, and the reconnect retry then replays the write: _upsert_node
bumps doc_freq a second time and _add_edge inserts another row, since
graph_edges has no uniqueness constraint for a logical edge. The chunk's
graph_ingest_progress row is now written in the same transaction as the rows it
describes, and a replay that finds it already "done" returns (0, 0) without
touching the graph. Extraction drops its separate mark_chunk("done"): the
checkpoint and the graph can no longer disagree.

count_nodes swallows every query failure and answers 0, so extraction's
"fall back to the write count" handler could never run — a failed count after a
successful build reported an empty graph. count_nodes grows a strict mode that
re-raises; retrieval keeps the swallow, which is what routes a source to
ClassicRAG.

A zero edge weight was read as a full-strength link: `or 1.0` rewrote an
explicit 0 before the <= 0 filter. Only missing and null weights default now.
The same coercion sat in _ppr_scores, where it would have kept the ranker's
rule unreachable from the product path, so it is fixed there too.

tests/graphrag/test_extraction.py

@@ -624,6 +624,42 @@ class TestSummaryNodeCount:
             store.delete_by_source(source_id)
 
 
+@pytest.mark.unit
+class TestSummaryCountFailure:
+    """A broken count query must not be reported as an empty graph."""
+
+    def test_a_failed_count_reports_the_write_count(
+        self, monkeypatch, stub_embedding
+    ):
+        from unittest.mock import MagicMock
+
+        store = MagicMock(name="GraphStore")
+        store.pending_chunks.return_value = ["c1"]
+        store.apply_chunk.return_value = (2, 1)
+        store.count_nodes.side_effect = RuntimeError("count query failed")
+        monkeypatch.setattr(
+            "docsgpt.graphrag.store.GraphStore", lambda *a, **k: store
+        )
+        _install_stub_llm(
+            monkeypatch,
+            _StubLLM([_extraction_json([{"name": "Ada"}], [])]),
+        )
+
+        summary = extract_graph_for_source(
+            str(uuid.uuid4()),
+            user="owner-1",
+            chunks=[_chunk("c1", "Ada.")],
+            config=SourceConfig(),
+            request_id="req-1",
+        )
+
+        # Falls back to what was actually written, not to zero.
+        assert summary["nodes"] == 2
+        # And it asked for a count that raises rather than one that returns 0,
+        # or the fallback above could never run.
+        assert store.count_nodes.call_args.kwargs.get("strict") is True
+
+
 @pytest.mark.unit
 class TestParsing:
     def test_parses_embedded_json(self):