port: sync from Mike/pygienium@63c2f73a

tests/deep-modules.test.ts

@@ -168,4 +168,17 @@ describe("deep-modules check", () => {
 			await rm(empty, { recursive: true, force: true }).catch(() => {});
 		}
 	});
+
+	it("does not skip when sources live in subdirectories (gate scans recursively)", async () => {
+		// Top level holds only a directory — the old shallow gate skipped any
+		// repo whose source lives under `game/`/`src/`-style subdirs.
+		await mkdir(join(cwd, "game"), { recursive: true });
+		await writeFile(join(cwd, "game", "main.lua"), "return {}\n", "utf8");
+		const check = getCheck("deep-modules")!;
+
+		await handleCheckCommand(check, "", stubCtx(cwd));
+
+		const state = await loadRunState(cwd);
+		expect(state?.checks["deep-modules"]?.status).toBe("complete");
+	});
 });