fix(bench): warmup + median for queryTimeMs to remove cold-start noise

scripts/benchmark.ts

@@ -133,9 +133,23 @@ const buildStart = performance.now();
 const buildResult = await buildGraph(root, { engine, incremental: false });
 const buildTimeMs = performance.now() - buildStart;
 
-const queryStart = performance.now();
-fnDepsData('buildGraph', dbPath);
-const queryTimeMs = performance.now() - queryStart;
+// Warmed median of QUERY_RUNS samples with `noTests: true` to match the
+// methodology used by query-benchmark.ts and the per-target `queries.*Ms`
+// block below. Earlier versions of this script measured a single cold call,
+// which conflated steady-state query latency with NAPI/rusqlite/OS-page-cache
+// init costs (~65ms on macOS) and inflated growth from test-fixture files
+// pulled in by new native extractors. See #1113 for the methodology rationale.
+const QUERY_WARMUP_RUNS = 3;
+for (let i = 0; i < QUERY_WARMUP_RUNS; i++) {
+	fnDepsData('buildGraph', dbPath, { depth: 3, noTests: true });
+}
+const queryTimings: number[] = [];
+for (let i = 0; i < QUERY_RUNS; i++) {
+	const start = performance.now();
+	fnDepsData('buildGraph', dbPath, { depth: 3, noTests: true });
+	queryTimings.push(performance.now() - start);
+}
+const queryTimeMs = median(queryTimings);
 
 const stats = statsData(dbPath);
 const totalFiles = stats.files.total;

tests/benchmarks/regression-guard.test.ts

@@ -188,16 +188,19 @@ const SKIP_VERSIONS = new Set(['3.8.0']);
  *   one-time bump as the cost of supporting Verilog. Tracked separately;
  *   exempt this release.
  *
- * - 3.10.0:Query time — cumulative effect of adding two native extractors
- *   (Solidity #1100 + R #1102) in quick succession. Neither tripped the
- *   threshold individually (Solidity PR's Query time stayed at 49ms, R PR
- *   showed no warning), but the combined +110% (49.6 → ~105ms) on the
- *   `fnDepsData('buildGraph', dbPath)` measurement reflects natural graph
- *   growth: ~1100 LoC of new extractor code + 9 fixture files added to the
- *   self-build benchmark expand `buildGraph`'s transitive callee count and
- *   DB row counts. Tracked in #1113 — exempt this release; remove once
- *   3.11.0+ data captures the new steady-state and the per-language
- *   fixture footprint has been evaluated.
+ * - 3.10.0:Query time — methodology artifact, not a real regression. The
+ *   metric was a single-shot cold call to `fnDepsData('buildGraph', dbPath)`
+ *   with no warmup, no median, and `noTests: false` — so it captured ~65ms
+ *   of NAPI/rusqlite/OS-page-cache init plus the cost of walking through
+ *   fixture files added by new language extractors. Local v3.9.6 vs HEAD
+ *   on the same corpus measured 78.8ms vs 67.5ms single-shot (HEAD faster),
+ *   while the warmed `queries.fnDepsMs` in the same benchmark showed 4.0ms
+ *   vs 2.8ms — confirming no underlying regression. Methodology fixed in
+ *   #1113: queryTimeMs now uses 3 warmup runs + median of 5 with
+ *   `noTests: true`, matching query-benchmark.ts hygiene. Exemption kept
+ *   in place until 3.11.0+ data captures the new steady-state under the
+ *   updated methodology (expected ~36ms native on this corpus); remove
+ *   the entry then.
  *
  * - 3.10.0:fnDeps depth 5 — same cause as Query time above. Merging main
  *   into #1102 added the Erlang extractor (#1103) on top of the existing