diff --git a/harness/src/eshost-elide/agent.elide.js b/harness/src/eshost-elide/agent.elide.js
index 9774324..94bad60 100644
--- a/harness/src/eshost-elide/agent.elide.js
+++ b/harness/src/eshost-elide/agent.elide.js
@@ -124,9 +124,9 @@ class ElideAgent extends ConsoleAgent {
       // test262 fixture files are ES modules by suite convention, but Elide
       // (Node-style) treats imported `.js` as CommonJS unless the enclosing
       // package declares `type: module`. Mark the temp dir accordingly for
-      // module-flagged tests (whose entry runs as `.mjs`, unaffected by the
-      // package type); remove the marker for script tests, whose `.js` entry
-      // must keep evaluating as a classic global script.
+      // module-flagged tests, whose `.js` entry then parses as ESM; remove the
+      // marker for script tests, whose `.js` entry must keep evaluating as a
+      // classic global script.
       const pkg = path.join(path.dirname(args[0]), "package.json");
       try {
         if (this._elideModule) {
diff --git a/harness/src/eshost-elide/agent.test.ts b/harness/src/eshost-elide/agent.test.ts
index 88cfc63..dbed3ff 100644
--- a/harness/src/eshost-elide/agent.test.ts
+++ b/harness/src/eshost-elide/agent.test.ts
@@ -84,7 +84,7 @@ test("_copyFixtures ignores specifiers that do not name real files", () => {
   expect(existsSync(join(dst, "missing_FIXTURE.js"))).toBe(false);
 });
 
-test("createChildProcess marks the temp dir type:module only for module tests", async () => {
+test("createChildProcess marks the temp dir type:module only for module tests and runs the entry in place", async () => {
   const dir = mkdtempSync(join(tmpdir(), "elide-agent-tmp-"));
   const entry = join(dir, "t.js");
   writeFileSync(entry, "// entry");
@@ -101,8 +101,10 @@ test("createChildProcess marks the temp dir type:module only for module tests",
     agent._elideModule = true;
     await agent.createChildProcess([entry]);
     expect(JSON.parse(readFileSync(join(dir, "package.json"), "utf8"))).toEqual({ type: "module" });
-    // Module entry runs as a `.mjs` copy.
-    expect(spawned[0][0]).toBe(join(dir, "t.mjs"));
+    // The module entry runs under its real `.js` name (parsed as ESM via the marker),
+    // so self/cyclic imports of that file dedupe to the single entry record.
+    expect(spawned[0][0]).toBe(entry);
+    expect(existsSync(join(dir, "t.mjs"))).toBe(false);
 
     agent._elideModule = false;
     await agent.createChildProcess([entry]);
diff --git a/harness/src/manifest.test.ts b/harness/src/manifest.test.ts
index 8837820..961a038 100644
--- a/harness/src/manifest.test.ts
+++ b/harness/src/manifest.test.ts
@@ -1,4 +1,10 @@
-import { existsSync, mkdtempSync, writeFileSync } from "node:fs";
+import { existsSync, mkdtempSync, readdirSync, writeFileSync } from "node:fs";
+
+// A checkout without submodules still has the empty suite directories, so test the
+// contents rather than the directory itself.
+function populated(dir: string): boolean {
+  return existsSync(dir) && readdirSync(dir).length > 0;
+}
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 import { test, expect } from "bun:test";
@@ -57,7 +63,7 @@ test("javac langtools manifest enables the full tools/javac tree", () => {
 
 test("cpython manifest entries exist in the checked-out CPython suite", () => {
   const suiteRoot = `${import.meta.dir}/../../suites/cpython`;
-  if (!existsSync(suiteRoot)) return;
+  if (!populated(suiteRoot)) return;
 
   const manifest = loadManifest(`${import.meta.dir}/../../manifests/cpython-core.toml`);
   const groups = new Map(manifest.groups.map((group) => [group.id, group.include]));
@@ -75,7 +81,7 @@ test("cpython manifest entries exist in the checked-out CPython suite", () => {
 
 test("wintertc WPT manifest includes checked-out paths when the suite exists", () => {
   const suiteRoot = `${import.meta.dir}/../../suites/wpt`;
-  if (!existsSync(suiteRoot)) return;
+  if (!populated(suiteRoot)) return;
 
   const manifest = loadManifest(`${import.meta.dir}/../../manifests/wintertc-wpt-2025.toml`);
   for (const path of manifest.groups.flatMap((group) => group.include)) {
diff --git a/harness/src/registry.test.ts b/harness/src/registry.test.ts
index 10c0b51..514d5a1 100644
--- a/harness/src/registry.test.ts
+++ b/harness/src/registry.test.ts
@@ -55,7 +55,7 @@ test("loads javac-jtreg workload from registry.toml", () => {
   expect(javac!.path).toBe("suites/openjdk");
   expect(javac!.settings.manifest).toBe("manifests/javac-langtools.toml");
   expect(javac!.settings.timeoutMs).toBe(3600000);
-  expect(javac!.settings.jtregCaseTimeoutSeconds).toBe(300);
+  expect(javac!.settings.jtregCaseTimeoutSeconds).toBe(900);
   expect(javac!.settings.javaRunner).toBe("java");
 });