port: sync from Mike/pygienium@63c2f73a

src/checks/deep-modules.ts

@@ -21,14 +21,13 @@
  * @module pygienium/checks/deep-modules
  */
 
-import { readdirSync } from "node:fs";
 import { join } from "node:path";
 import {
 	registerCheck,
 	type CheckDefinition,
 	type CheckScope,
 } from "./registry.js";
-import { isScopeSource, scopeRulesMarkdown } from "./scope.js";
+import { hasScopeSources, scopeRulesMarkdown } from "./scope.js";
 
 /** Output directory for this check's persistent reports. */
 export function deepModulesOutputDir(cwd: string): string {
@@ -50,23 +49,13 @@ export function changesPath(cwd: string): string {
  * with zero source files gives the scanner nothing to classify.
  */
 function deepModulesGate(cwd: string): string | undefined {
-	let found = false;
 	try {
-		const entries = readdirSync(cwd);
+		if (hasScopeSources(cwd)) return undefined;
-		for (const entry of entries) {
-			if (isScopeSource(entry)) {
-				found = true;
-				break;
-			}
-		}
 	} catch {
 		// unreadable cwd → let the agent decide; don't block.
 		return undefined;
 	}
-	if (!found) {
 	return "no source files found to inspect";
-	}
-	return undefined;
 }
 
 /**

src/checks/defensive-guards.ts

@@ -41,14 +41,13 @@
  * @module pygienium/checks/defensive-guards
  */
 
-import { readdirSync } from "node:fs";
 import { join } from "node:path";
 import {
 	registerCheck,
 	type CheckDefinition,
 	type CheckScope,
 } from "./registry.js";
-import { isScopeSource, scopeRulesMarkdown } from "./scope.js";
+import { hasScopeSources, scopeRulesMarkdown } from "./scope.js";
 
 /** Output directory for this check's persistent reports. */
 export function defensiveGuardsOutputDir(cwd: string): string {
@@ -70,23 +69,13 @@ export function changesPath(cwd: string): string {
  * with zero source files gives the scanner nothing to analyse.
  */
 function defensiveGuardsGate(cwd: string): string | undefined {
-	let found = false;
 	try {
-		const entries = readdirSync(cwd);
+		if (hasScopeSources(cwd)) return undefined;
-		for (const entry of entries) {
-			if (isScopeSource(entry)) {
-				found = true;
-				break;
-			}
-		}
 	} catch {
 		// unreadable cwd → let the agent decide; don't block.
 		return undefined;
 	}
-	if (!found) {
 	return "no source files found to inspect";
-	}
-	return undefined;
 }
 
 /**

src/checks/scope.ts

@@ -9,6 +9,10 @@
  * @module pygienium/checks/scope
  */
 
+import { readdirSync, statSync } from "node:fs";
+import type { Dirent } from "node:fs";
+import { join } from "node:path";
+
 /**
  * Implementation-code file extensions pygienium inspects.
  *
@@ -106,6 +110,38 @@ export function isScopeSource(path: string): boolean {
 	return SCOPE_EXTENSIONS.has(lower.slice(dot));
 }
 
+/**
+ * True when the tree rooted at `root` contains at least one in-scope source
+ * file. Walks recursively (honoring {@link SCOPE_EXCLUDE_DIRS}) — a top-level
+ * entry scan alone would skip any repo whose source lives in subdirectories,
+ * e.g. `game/` or `src/`, even though recon's git inventory finds hundreds of
+ * files. A file root is judged by {@link isScopeSource} directly.
+ */
+export function hasScopeSources(root: string): boolean {
+	const st = statSync(root, { throwIfNoEntry: false });
+	if (!st) return false;
+	if (st.isFile()) return isScopeSource(root);
+	const stack = [root];
+	while (stack.length > 0) {
+		const dir = stack.pop() as string;
+		let entries: Dirent[];
+		try {
+			entries = readdirSync(dir, { withFileTypes: true });
+		} catch {
+			continue;
+		}
+		for (const entry of entries) {
+			if (entry.isDirectory()) {
+				if (SCOPE_EXCLUDE_DIRS.has(entry.name)) continue;
+				stack.push(join(dir, entry.name));
+			} else if (entry.isFile() && isScopeSource(entry.name)) {
+				return true;
+			}
+		}
+	}
+	return false;
+}
+
 /**
  * Markdown section injected into every scan task string so the sub-agent knows
  * exactly what to inspect and what to skip — stated once here, not copy-pasted

src/checks/todos.ts

@@ -36,7 +36,6 @@
  * @module pygienium/checks/todos
  */
 
-import { readdirSync } from "node:fs";
 import { readFile, readdir, stat } from "node:fs/promises";
 import { join, relative } from "node:path";
 import { loadRunState } from "../run-state.js";
@@ -46,6 +45,7 @@ import {
 	type CheckScope,
 } from "./registry.js";
 import {
+	hasScopeSources,
 	isScopeSource,
 	SCOPE_EXCLUDE_DIRS,
 	scopeRulesMarkdown,
@@ -405,23 +405,13 @@ function renderFindings(
  * with zero source files gives the scanner nothing to analyse.
  */
 function todosGate(cwd: string): string | undefined {
-	let found = false;
 	try {
-		const entries = readdirSync(cwd);
+		if (hasScopeSources(cwd)) return undefined;
-		for (const entry of entries) {
-			if (isScopeSource(entry)) {
-				found = true;
-				break;
-			}
-		}
 	} catch {
 		// unreadable cwd → let the agent decide; don't block.
 		return undefined;
 	}
-	if (!found) {
 	return "no source files found to inspect";
-	}
-	return undefined;
 }
 
 /**

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");
+	});
 });

tests/defensive-guards.test.ts

@@ -229,4 +229,17 @@ describe("defensive-guards check", () => {
 		const state = await loadRunState(cwd);
 		expect(state?.checks["defensive-guards"]?.status).toBe("skipped");
 	});
+
+	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("defensive-guards")!;
+
+		await handleCheckCommand(check, "", stubCtx(cwd));
+
+		const state = await loadRunState(cwd);
+		expect(state?.checks["defensive-guards"]?.status).toBe("complete");
+	});
 });

tests/todos.test.ts

@@ -335,6 +335,19 @@ describe("todos check", () => {
 		expect(state?.checks["todos"]?.status).toBe("skipped");
 	});
 
+	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("todos")!;
+
+		await handleCheckCommand(check, "", stubCtx(cwd));
+
+		const state = await loadRunState(cwd);
+		expect(state?.checks["todos"]?.status).toBe("complete");
+	});
+
 	it("reports a new/resolved delta against the previous run's counts", async () => {
 		await seedStubs(cwd);
 		const check = getCheck("todos")!;