test: fix two parallelism-exposed flakes (probe re-run, live-tree census)

Both pass solo and on main but flaked under the parallel runner:

1. gstack-brain-context-load probed 'gbrain --version' PER QUERY with a
   500ms budget — a cold probe on a saturated box timed out (observed
   505ms), branding gbrain 'missing' for one query while siblings
   passed. The probe is now memoized (availability can't change
   mid-invocation) with a generous one-time 5s budget; query calls keep
   the tight timeout.

2. skill-size-budget's catalog estimate read the LIVE tree, so a
   concurrent worker's transient skill-shaped scratch dirs exactly
   doubled it (8356 vs 4177). The ratchet now counts git-TRACKED skills
   only — the catalog that ships, immune to sibling workers.

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

bin/gstack-brain-context-load.ts

@@ -190,16 +190,26 @@ function resolveSkillFile(args: CliArgs): string | null {
 
 // ── Dispatchers ────────────────────────────────────────────────────────────
 
+// Memoized: availability can't change mid-invocation, and the per-query
+// re-probe was both wasteful (N probes per run) and load-flaky — a cold
+// `gbrain --version` on a saturated box can exceed the 500ms budget, branding
+// gbrain "missing" for one query while its siblings succeed (observed under
+// the parallel free-suite runner: SKIP at dur=505ms with two OKs after it).
+let _gbrainAvailable: boolean | null = null;
 function gbrainAvailable(): boolean {
+  if (_gbrainAvailable !== null) return _gbrainAvailable;
   try {
     execFileSync("gbrain", ["--version"], {
       stdio: "ignore",
-      timeout: MCP_TIMEOUT_MS,
+      // Generous first-probe budget: this runs ONCE, and a slow-to-start CLI
+      // is not a missing CLI. Query calls keep the tight MCP_TIMEOUT_MS.
+      timeout: 5_000,
     });
-    return true;
+    _gbrainAvailable = true;
   } catch {
-    return false;
+    _gbrainAvailable = false;
   }
+  return _gbrainAvailable;
 }
 
 function dispatchVector(q: GbrainManifestQuery, args: CliArgs): QueryResult {