perf(resolution): defer checkpoints and double-buffer persist during resolution, byte-identical graphs (#1320)

Fresh init on a 4,402-file Java repo (dubbo): 18.2s -> 13.5s (-26%), with
the resolution phase going 12.6s -> 7.9s (-38%). Graphs verified
byte-identical on both the pool path (dubbo) and the sequential path
(excalidraw).

Two changes:

1. The fastInit+pool path restored WAL for the resolver workers but left
   wal_autocheckpoint at its default, so the persist loop inline-checkpointed
   hot pages all phase long (#1231's pathology inside resolution — measured
   at 58% of resolution wall). Checkpointing is now deferred behind the
   bounded valve and folded once at maintenance, mirroring the deferWal path.

2. The resolution loop is double-buffered: batch k+1 is prefetched (OFFSET
   past batch k's still-pending rows, under an explicit ORDER BY rowid) and
   fanned out across the pool while batch k's ref cleanup runs on the main
   thread. Batch settle-waits dropped 2572ms -> 117ms.

Correctness invariant found by the byte-identical gate and now documented in
the loop: batch k+1's resolution READS batch k's edges (resolveMethodOnType
walks supertype chains over extends/implements edges that resolution itself
inserts), so edges must persist BEFORE the next batch fans out; only the ref
cleanup overlaps.

Also extends the CODEGRAPH_SYNTH_TIMINGS instrumentation with phase labels
(grammar-init, parse-loop, fts-rebuild, resolver-reinit, resolution,
callback-synthesis) and pool timings (worker open/resolve, per-batch mode,
persist), so the next profile is one env var away.

Suite green (2444). Sync path timings unchanged. Pool floor re-validated:
forced-on at 40k refs is still net-slower, so the 150k threshold stands.

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

src/extraction/index.ts

@@ -1520,7 +1520,9 @@ export class ExtractionOrchestrator {
     // in file order preserves the #1015 determinism exactly.
     storeWriterOpts?: { dbPath: string; fastInit: boolean } | null
   ): Promise<IndexResult> {
+    const tGrammar = Date.now();
     await initGrammars();
+    if (process.env.CODEGRAPH_SYNTH_TIMINGS) console.error(`[phase-timing] grammar-init: ${Date.now() - tGrammar}ms`);
     const startTime = Date.now();
     const errors: ExtractionError[] = [];
     let filesIndexed = 0;
@@ -1816,6 +1818,7 @@ export class ExtractionOrchestrator {
       }
     };
 
+    const tParseLoop = Date.now();
     for (let i = 0; i < files.length; i += FILE_IO_BATCH_SIZE) {
       if (signal?.aborted) { aborted = true; break; }
 
@@ -1907,6 +1910,7 @@ export class ExtractionOrchestrator {
         }
       }
     }
+    if (process.env.CODEGRAPH_SYNTH_TIMINGS) console.error(`[phase-timing] parse-loop: ${Date.now() - tParseLoop}ms`);
 
     if (signal?.aborted || aborted) {
       if (storeWriter) await storeWriter.close();