CG-33: converge incremental sync with a full rebuild

A live, auto-synced index did not converge to a clean rebuild of the same
tree — 4.3% of distinct edges wrong in both directions on this repo's own
index, overwhelmingly `calls`, which is what flow queries traverse and what
explore's file ranking weights. Silent: nothing warned, and the symptom read
as "codegraph isn't very good" rather than "this index needs rebuilding."

Two causes, and the fix needed both. Resolution binds a reference to one of
the same-named definitions PROJECT-WIDE, so a definition appearing or
vanishing changes the correct answer for references in files the sync never
touches — and those references resolved successfully once, which deletes
their unresolved_refs row, leaving nothing to revisit them with (#1240's
retry only revisits refs parked as failed). Separately, when nothing
disambiguated the candidates the winner came down to rowid, i.e. the order
files happened to be WRITTEN, which differs between a scan-order full index
and a sync that appends each file as it changes. That second one is why
re-resolution alone could not converge: re-resolving against the identical
graph still picked a different candidate.

So getNodesByName now orders by (file_path, start_line) — a property of the
code, not of the write order — and sync computes a definitionDelta and
re-opens the resolution edges whose answer it may have invalidated,
re-inserting each as the reference that created it for the orphan sweep to
bind against the post-sync graph.

The delta compares `file\0name` pairs per file rather than one name set over
the batch: a commit that adds `collect` to a new file while an unrelated
changed file already defines `collect` cancels out of a batch-wide set, and
that miss was the largest residual class in the first measurement.

Conservative where the failure modes are asymmetric — a wrong deletion is a
permanent edge loss, a missed rebind is only residual drift. Edges without a
refName stamp are never touched (nothing to restore them from), sources the
sync already re-extracted are skipped, and a per-name ceiling declines the
generic names. Edges are deleted before the sweep re-inserts, since
INSERT OR IGNORE against idx_edges_identity would otherwise keep both rows
when a reference rebinds elsewhere.

Replaying real commits of this repo through sync, then diffing against a
rebuild: 16 commits 48 -> 0; 80 commits 1,634 -> 361, with the actively
misleading direction (stale edges the index keeps asserting) 671 -> 2.
Index and sync wall-clock are unchanged; the ORDER BY costs 18% per uncached
name lookup, which never reaches wall-clock because the resolver memoizes it.

The 357-edge residual at 80 commits is one pre-existing class: refs to
generic names (`push`, `join`) parked above #1240's per-name retry ceiling,
which a rebuild resolves into cross-language garbage — a TS test file
"calling" an R method. Converging there would mean manufacturing wrong edges,
so it is left alone. And no drift metric in `codegraph status`: it cannot be
computed without the rebuild it would be recommending, and a proxy would fire
on that residual and train users to ignore it.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

src/index.ts

@@ -883,6 +883,32 @@ export class CodeGraph {
           }
         }
 
+        // Re-open resolution edges this sync may have invalidated ELSEWHERE in
+        // the repo (CG-33). Everything above re-resolves references in the
+        // changed files; this covers the opposite direction — references in
+        // files the sync never touched whose answer depended on a definition
+        // that just appeared or disappeared. Without it a synced index never
+        // converges to a full rebuild: measured at 4.3% of distinct edges wrong
+        // on codegraph's own index, in both directions, mostly `calls`. The
+        // resurrected refs are pending rows, so the orphan sweep immediately
+        // below is what resolves them — batched, yielding, multi-pass, exactly
+        // as a full index resolves.
+        //
+        // `definitionDelta` is empty for a body-only edit, so the overwhelmingly
+        // common sync pays one branch. CODEGRAPH_NO_REBIND=1 disables it.
+        if (result.definitionDelta && process.env.CODEGRAPH_NO_REBIND !== '1') {
+          const tRebind = Date.now();
+          const rebound = this.orchestrator.resurrectStaleResolutionEdges(
+            result.definitionDelta,
+            result.changedFilePaths ?? []
+          );
+          if (process.env.CODEGRAPH_SYNTH_TIMINGS) {
+            console.error(
+              `[phase-timing] sync-rebind: ${Date.now() - tRebind}ms (${result.definitionDelta.length} changed names, ${rebound} edges re-opened)`
+            );
+          }
+        }
+
         // Orphan sweep (#1187). A resolution pass that dies mid-run — the #850
         // daemon liveness watchdog's SIGKILL (#1122), Ctrl-C, a crash — leaves
         // the refs it never reached in unresolved_refs, and the git-scoped fast