fix(brain-context): cold-start probe latency permanently disabled gbrain context

gbrainAvailable() spawned gbrain --version under a 500ms budget; a cold CLI
start on a loaded machine blew the timeout, misclassified gbrain as missing,
and every skill session silently ran brainless — plus the per-query re-probe
burned 3x the budget before any real work. Replaced with a memoized
stat-based PATH scan (PATHEXT-aware on Windows) and made the query timeout
overridable via GSTACK_BRAIN_TIMEOUT_MS for loaded CI environments.

Also picks up the fork's manifest-filter coverage (#1687 shape) against the
fake-gbrain harness — passes against our existing filter support.

Ported from time-attack/gstack (GStack 2).

Co-authored-by: Sina Matian <sina@time-attack.dev>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

bin/gstack-brain-context-load.ts

@@ -34,9 +34,9 @@
  *   gstack-brain-context-load --quiet
  */
 
-import { existsSync, readFileSync, statSync, readdirSync } from "fs";
-import { join, dirname, basename, resolve } from "path";
-import { execFileSync, spawnSync } from "child_process";
+import { existsSync, readFileSync, statSync, readdirSync, accessSync, constants } from "fs";
+import { join, dirname, basename, resolve, delimiter } from "path";
+import { spawnSync } from "child_process";
 import { homedir } from "os";
 
 import { parseSkillManifest, type GbrainManifest, type GbrainManifestQuery, withErrorContext } from "../lib/gstack-memory-helpers";
@@ -68,7 +68,9 @@ interface QueryResult {
 
 const HOME = homedir();
 const GSTACK_HOME = process.env.GSTACK_HOME || join(HOME, ".gstack");
-const MCP_TIMEOUT_MS = 500;
+// 500ms hard cap per Section 1C; overridable for slow/loaded environments
+// (test harnesses under CI load, cold CLI starts).
+const MCP_TIMEOUT_MS = Math.max(1, parseInt(process.env.GSTACK_BRAIN_TIMEOUT_MS || "", 10) || 500);
 const PAGE_SIZE_CAP = 10 * 1024; // 10KB per query result before truncation
 
 // ── CLI ────────────────────────────────────────────────────────────────────
@@ -190,16 +192,28 @@ function resolveSkillFile(args: CliArgs): string | null {
 
 // ── Dispatchers ────────────────────────────────────────────────────────────
 
+let gbrainOnPath: boolean | null = null;
+
 function gbrainAvailable(): boolean {
-  try {
-    execFileSync("gbrain", ["--version"], {
-      stdio: "ignore",
-      timeout: MCP_TIMEOUT_MS,
-    });
-    return true;
-  } catch {
-    return false;
-  }
+  // Stat-based PATH scan, memoized. Spawning `gbrain --version` under the
+  // 500ms budget misreported gbrain as missing whenever a cold process spawn
+  // exceeded the timeout (loaded machine, node-based CLI cold start), and
+  // re-probing per query burned 3x the budget before any real work.
+  if (gbrainOnPath !== null) return gbrainOnPath;
+  const exts = process.platform === "win32"
+    ? (process.env.PATHEXT || ".COM;.EXE;.BAT;.CMD").split(";")
+    : [""];
+  gbrainOnPath = (process.env.PATH || "").split(delimiter).some((dir) =>
+    dir !== "" && exts.some((ext) => {
+      try {
+        accessSync(join(dir, `gbrain${ext}`), constants.X_OK);
+        return true;
+      } catch {
+        return false;
+      }
+    })
+  );
+  return gbrainOnPath;
 }
 
 function dispatchVector(q: GbrainManifestQuery, args: CliArgs): QueryResult {

test/gstack-brain-context-load.test.ts

@@ -55,7 +55,12 @@ fi
 function prependPath(binDir: string): Record<string, string> {
   const pathKey = Object.keys(process.env).find((key) => key.toLowerCase() === "path") || "PATH";
   const currentPath = process.env[pathKey] || "";
-  return { [pathKey]: `${binDir}${delimiter}${currentPath}` };
+  return {
+    [pathKey]: `${binDir}${delimiter}${currentPath}`,
+    // Cold process spawns on a loaded machine can exceed the 500ms default
+    // budget; the fake gbrain is instant once spawned, so give it headroom.
+    GSTACK_BRAIN_TIMEOUT_MS: "10000",
+  };
 }
 
 describe("gstack-brain-context-load CLI", () => {
@@ -252,6 +257,44 @@ describe("gstack-brain-context-load — graceful gbrain absence", () => {
     }
   });
 
+  it("manifest filter: blocks reach gbrain as --filter args with template vars resolved (#1687)", () => {
+    const dir = mkdtempSync(join(tmpdir(), "gstack-bcl-"));
+    const binDir = join(dir, "bin");
+    mkdirSync(binDir);
+    writeFakeGbrain(binDir);
+    const skillFile = join(dir, "SKILL.md");
+    writeFileSync(
+      skillFile,
+      `---
+name: x
+gbrain:
+  schema: 1
+  context_queries:
+    - id: prior-sessions
+      kind: list
+      filter:
+        type: ceo-plan
+        tags_contains: "repo:{repo_slug}"
+      sort: updated_at_desc
+      limit: 5
+      render_as: "## Prior sessions"
+---
+`,
+      "utf-8"
+    );
+
+    try {
+      const r = runScript(["--skill-file", skillFile, "--repo", "my-test-repo"], prependPath(binDir));
+      expect(r.exitCode).toBe(0);
+      expect(r.stdout).toContain("fake gbrain list_pages");
+      expect(r.stdout).toContain("--filter type=ceo-plan");
+      expect(r.stdout).toContain("--filter tags_contains=repo:my-test-repo");
+      expect(r.stdout).toContain("--sort updated_at_desc");
+    } finally {
+      rmSync(dir, { recursive: true, force: true });
+    }
+  });
+
   it("vector + list queries still complete (with SKIP) when gbrain CLI is missing", () => {
     // We can't easily un-install gbrain; rely on the helper's own missing-binary
     // detection. The default manifest uses kind: list which calls gbrain. If