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.

docsgpt/graphrag/extraction.py

@@ -290,7 +290,9 @@ def extract_graph_for_source(
             )
             node_upserts += chunk_nodes
             edges += chunk_edges
-            store.mark_chunk(source_id, chunk_id, "done")
+            # ``apply_chunk`` marks the chunk done inside the transaction that
+            # writes its rows, so the checkpoint cannot disagree with the graph
+            # and a replayed write cannot apply the chunk twice.
             chunks_processed += 1
         except Exception as exc:
             logger.warning(
@@ -311,9 +313,12 @@ def extract_graph_for_source(
     # upserts and a single node, so the old count overstated every graph whose
     # entities recur. Report what the graph holds, falling back to the write
     # count only if the count query itself fails.
+    # ``strict`` is what makes the fallback below reachable: the default
+    # count swallows query failures and answers 0, which would report a
+    # successful build as an empty graph.
     nodes = node_upserts
     try:
-        nodes = store.count_nodes(source_id)
+        nodes = store.count_nodes(source_id, strict=True)
     except Exception as exc:
         logger.warning(
             "count_nodes failed for source %s; reporting upserts instead: %s",