fix(resolution): clean up processed refs by row id so batch boundaries can't drop sibling call sites (#1269) (#1270)

Post-batch cleanup deleted resolved refs (and parked failed ones) by
(from_node_id, reference_name, reference_kind) — no line/col. When one
caller had several call sites to the same callee and a batch boundary
split them, the first batch's cleanup removed every row with that key,
including later-batch siblings that were never attempted — their edges
were silently never created. On nlohmann/json this ate 422 real call
edges (write_cbor's 38 to_char_type calls indexed as 11).

Refs loaded from unresolved_refs now carry their row id through
resolution, and all three persist paths (sync resolveAndPersist, the
yielding retry pass, the batched drain loop) delete / mark-failed by
exactly that id. The key-tuple methods remain only as the fallback for
hand-built refs from the public API. Failed-parking gains the same
precision: outcome can differ per call site (receiver inference reads
the ref's line), so a sibling must not inherit another row's failure.

Also untracks the zz-scratch local test files that slipped into #1268
and gitignores the pattern.

Validation: red-green regression test (5 sites, batch size 2 — old code
kept 2 edges, fix keeps 5); nlohmann/json re-index is a strict superset
of the previous edge set (0 lost, 422 recovered, spot-checked against
source).

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

.gitignore

@@ -70,3 +70,6 @@ assets/__pycache__/
 assets/generate-waitlist.py
 
 .kommandr/
+
+# Local scratch tests (never commit)
+__tests__/zz-scratch*