diff --git a/tests2/harness/file-boundary-runner.ts b/tests2/harness/file-boundary-runner.ts
new file mode 100644
index 000000000..ecc1dc5ef
--- /dev/null
+++ b/tests2/harness/file-boundary-runner.ts
@@ -0,0 +1,17 @@
+import { VitestTestRunner } from "vitest/runners";
+import type { File } from "@vitest/runner";
+import { setProjectRoot } from "../../src/server/bobbit-dir.js";
+import { resetAgentDirStateForTests } from "../../src/server/agent-dir-config.js";
+
+const BASELINE_CWD = process.cwd();
+
+// isolate:false files share a fork's module graph, so the project-root and
+// agent-dir singletons leak between files. onCollectStart is the only hook that
+// runs per file before its module loads; env is left to the fork-scoped gateway.
+export default class FileBoundaryRunner extends VitestTestRunner {
+	onCollectStart(file: File): void {
+		setProjectRoot(BASELINE_CWD);
+		resetAgentDirStateForTests();
+		return super.onCollectStart(file);
+	}
+}
diff --git a/vitest.config.ts b/vitest.config.ts
index 374cfe7d4..9e1f3e4bb 100644
--- a/vitest.config.ts
+++ b/vitest.config.ts
@@ -50,6 +50,8 @@ const shared = {
 	},
 };
 const tier1SetupFiles = ["tests2/harness/tier1-spawn-guard.ts"];
+// Per-file reset of leaking dir singletons for the isolate:false projects.
+const fileBoundaryRunner = "tests2/harness/file-boundary-runner.ts";
 
 const coverage = {
 	provider: "v8" as const,
@@ -99,6 +101,7 @@ export default defineConfig({
 					...shared,
 					name: "v2-core",
 					environment: "node",
+					runner: fileBoundaryRunner,
 					setupFiles: tier1SetupFiles,
 					include: execution.core,
 				},
@@ -123,6 +126,7 @@ export default defineConfig({
 					...shared,
 					name: "v2-integration",
 					environment: "node",
+					runner: fileBoundaryRunner,
 					setupFiles: tier1SetupFiles,
 					include: execution.integration,
 					testTimeout: 60_000,