yoyo: Remove flat-directory fallback from getOnDiskSlugs in lint-checks.ts

src/lib/__tests__/lint-checks.test.ts

@@ -84,31 +84,31 @@ describe("getOnDiskSlugs", () => {
     expect(slugs.sort()).toEqual(["alpha", "beta"]);
   });
 
-  it("returns slugs from .md files excluding index.md and log.md (fallback)", async () => {
+  it("returns empty array when page-index is absent even if .md files exist", async () => {
     const wikiDir = process.env.WIKI_DIR!;
     await fs.writeFile(path.join(wikiDir, "alpha.md"), "# Alpha\n\nContent");
     await fs.writeFile(path.join(wikiDir, "beta.md"), "# Beta\n\nContent");
     await fs.writeFile(path.join(wikiDir, "index.md"), "# Index\n\n- alpha");
     await fs.writeFile(path.join(wikiDir, "log.md"), "# Log\n\n- entry");
 
     const slugs = await getOnDiskSlugs();
-    expect(slugs.sort()).toEqual(["alpha", "beta"]);
+    expect(slugs).toEqual([]);
   });
 
   it("returns empty array when directory does not exist", async () => {
     const slugs = await getOnDiskSlugs();
     expect(slugs).toEqual([]);
   });
 
-  it("ignores non-.md files (fallback)", async () => {
+  it("returns empty array when page-index is absent regardless of file types on disk", async () => {
     const wikiDir = process.env.WIKI_DIR!;
     await fs.writeFile(path.join(wikiDir, "page.md"), "# Page\n\nContent");
     await fs.writeFile(path.join(wikiDir, "readme.txt"), "Not a wiki page");
     await fs.writeFile(path.join(wikiDir, "data.json"), "{}");
     await fs.writeFile(path.join(wikiDir, ".hidden"), "secret");
 
     const slugs = await getOnDiskSlugs();
-    expect(slugs).toEqual(["page"]);
+    expect(slugs).toEqual([]);
   });
 
   it("returns empty array for an empty directory", async () => {

src/lib/__tests__/lint.test.ts

@@ -4,7 +4,7 @@ import os from "os";
 import path from "path";
 import { writeWikiPage, updateIndex, ensureDirectories, readLog } from "../wiki";
 import type { IndexEntry } from "../types";
-import { _resetStorage } from "../storage";
+import { _resetStorage, getStorage } from "../storage";
 
 // Mock the LLM module so lint never calls the real API
 vi.mock("../llm", () => ({
@@ -90,6 +90,9 @@ describe("lint", () => {
       { slug: "hello", title: "Hello", summary: "A greeting page" },
     ];
     await updateIndex(entries);
+    await getStorage().putIndex("pages", {
+      "hello": { slug: "hello", title: "Hello", summary: "A greeting page" },
+    });
 
     const result = await lint();
 
@@ -109,6 +112,9 @@ describe("lint", () => {
     );
     // Create an empty index with no entries
     await updateIndex([]);
+    await getStorage().putIndex("pages", {
+      "orphan": { slug: "orphan", title: "Orphan", summary: "s" },
+    });
 
     const result = await lint();
     const orphanIssues = result.issues.filter((i) => i.type === "orphan-page");
@@ -140,6 +146,9 @@ describe("lint", () => {
       { slug: "empty", title: "Empty Page", summary: "Barely anything here" },
     ];
     await updateIndex(entries);
+    await getStorage().putIndex("pages", {
+      "empty": { slug: "empty", title: "Empty Page", summary: "Barely anything here" },
+    });
 
     const result = await lint();
     const emptyIssues = result.issues.filter((i) => i.type === "empty-page");
@@ -164,6 +173,10 @@ describe("lint", () => {
       { slug: "beta", title: "Beta Topic", summary: "Beta page" },
     ];
     await updateIndex(entries);
+    await getStorage().putIndex("pages", {
+      "alpha": { slug: "alpha", title: "Alpha", summary: "Alpha page" },
+      "beta": { slug: "beta", title: "Beta Topic", summary: "Beta page" },
+    });
 
     const result = await lint();
     const crossRefIssues = result.issues.filter(
@@ -277,6 +290,10 @@ describe("lint", () => {
       { slug: "neural-network", title: "Neural Network", summary: "NN page" },
     ];
     await updateIndex(entries);
+    await getStorage().putIndex("pages", {
+      "intro": { slug: "intro", title: "Intro", summary: "Intro page" },
+      "neural-network": { slug: "neural-network", title: "Neural Network", summary: "NN page" },
+    });
 
     const result = await lint();
     const crossRefIssues = result.issues.filter(
@@ -905,6 +922,10 @@ Every page must start with a level-1 heading.
       { slug: "transformer", title: "Transformer", summary: "Test" },
       { slug: "bert", title: "BERT", summary: "Test" },
     ]);
+    await getStorage().putIndex("pages", {
+      "transformer": { slug: "transformer", title: "Transformer", summary: "Test" },
+      "bert": { slug: "bert", title: "BERT", summary: "Test" },
+    });
 
     const result = await lint();
     const conceptIssues = result.issues.filter(
@@ -989,6 +1010,9 @@ Every page must start with a level-1 heading.
     await updateIndex([
       { slug: "linker", title: "Linker", summary: "Test" },
     ]);
+    await getStorage().putIndex("pages", {
+      "linker": { slug: "linker", title: "Linker", summary: "Test" },
+    });
 
     const result = await lint();
     const brokenLinkIssues = result.issues.filter(
@@ -1069,6 +1093,9 @@ describe("lint with LintOptions", () => {
       { slug: "ghost", title: "Ghost", summary: "Does not exist on disk" },
     ];
     await updateIndex(entries);
+    await getStorage().putIndex("pages", {
+      "orphan-only": { slug: "orphan-only", title: "Orphan Only", summary: "s" },
+    });
 
     const result = await lint({ checks: ["orphan-page"] });
 

src/lib/__tests__/maintenance.test.ts

@@ -12,7 +12,7 @@ import {
 import { createThread, addComment } from "../talk";
 import { scanForMaintenance, rebuildDerivedIndexes } from "../maintenance";
 import { listCommonsPages } from "../commons";
-import { _resetStorage } from "../storage";
+import { _resetStorage, getStorage } from "../storage";
 
 let tmpDir: string;
 const saved: Record<string, string | undefined> = {};
@@ -241,6 +241,10 @@ describe("scanForMaintenance", () => {
       path.join(wikiDir, "orphan-page.md"),
       "# Orphan\n\nThis page exists on disk but is not in the index.",
     );
+    await getStorage().putIndex("pages", {
+      "indexed-page": { slug: "indexed-page", title: "indexed-page", summary: "s" },
+      "orphan-page": { slug: "orphan-page", title: "Orphan", summary: "s" },
+    });
     const tasks = await scanForMaintenance();
     expect(tasks).toContainEqual({
       kind: "maintain",
@@ -334,6 +338,10 @@ describe("scanForMaintenance", () => {
       logOp: "ingest",
       crossRefSource: null,
     });
+    await getStorage().putIndex("pages", {
+      "artificial-intelligence": { slug: "artificial-intelligence", title: "Artificial Intelligence", summary: "s" },
+      "machine-learning": { slug: "machine-learning", title: "Machine Learning", summary: "s" },
+    });
     const tasks = await scanForMaintenance();
     expect(tasks).toContainEqual({
       kind: "maintain",

src/lib/__tests__/mcp.test.ts

@@ -53,7 +53,7 @@ import {
 } from "../../mcp";
 import { vaultIdFor, listVaults, getVault, createVault } from "../vault";
 import { readWikiPageWithFrontmatter } from "../wiki";
-import { _resetStorage } from "../storage";
+import { _resetStorage, getStorage } from "../storage";
 import { _resetConfigCache } from "../config";
 import { parseFrontmatter } from "../frontmatter";
 import { registerAgent } from "../agents";
@@ -2496,6 +2496,11 @@ describe("lint_wiki", () => {
     );
     await writeIndex([]); // empty index
 
+    // Seed page-index so getOnDiskSlugs() sees the orphan page
+    await getStorage().putIndex("pages", {
+      "orphan-page": { slug: "orphan-page", title: "Orphan Page", summary: "s" },
+    });
+
     const result = await handleLintWiki({ checks: ["orphan-page"] });
     expect(result.issues.length).toBeGreaterThanOrEqual(1);
     const orphanIssues = result.issues.filter((i) => i.type === "orphan-page");
@@ -4782,6 +4787,11 @@ describe("maintenance_scan", () => {
     );
     await writeIndex([]); // empty index → orphan-maint is an orphan
 
+    // Seed page-index so getOnDiskSlugs() sees the orphan page
+    await getStorage().putIndex("pages", {
+      "orphan-maint": { slug: "orphan-maint", title: "Orphan Maintenance", summary: "s" },
+    });
+
     const result = await handleMaintenanceScan({});
     expect(result).toHaveProperty("tasks");
     expect(Array.isArray(result.tasks)).toBe(true);

src/lib/lint-checks.ts

@@ -1,6 +1,4 @@
-import { getStorage } from "./storage";
-import type { FileEntry } from "./storage";
-import { readWikiPage, readWikiPageWithFrontmatter, listWikiPages, wikiRelPath } from "./wiki";
+import { readWikiPage, readWikiPageWithFrontmatter, listWikiPages } from "./wiki";
 import { hasLLMKey, callLLM } from "./llm";
 import { loadPageConventions } from "./schema";
 import { extractWikiLinks } from "./links";
@@ -38,35 +36,19 @@ export const INFRASTRUCTURE_FILES = new Set(["index.md", "log.md"]);
 /**
  * Get all content page slugs known to the system.
  *
- * Primary path: read from the `_idx:pages` page-index (O(1) KV read), which
- * aligns lint with the silo-primary read path used by `readWikiPage` /
- * `listWikiPages`.
- *
- * Fallback (page-index not yet seeded): list `.md` files from the flat wiki
- * directory, excluding infrastructure files. This preserves correct orphan /
- * stale-index detection before the first `rebuildPageIndex()` run.
- *
+ * Reads from the `_idx:pages` page-index (O(1) KV read), which aligns lint
+ * with the silo-primary read path used by `readWikiPage` / `listWikiPages`.
+ * Returns `[]` when the page-index is absent or unreadable.
  */
 export async function getOnDiskSlugs(): Promise<string[]> {
   try {
     const idx = await getPageIndex();
     if (idx) return Object.keys(idx);
   } catch (err) {
-    logger.warn("lint", "page-index read failed; falling back to listFiles", err);
-  }
-
-  // Fallback: list flat wiki directory
-  let entries: FileEntry[];
-  try {
-    entries = await getStorage().listFiles(wikiRelPath(""));
-  } catch (err) {
-    logger.warn("lint", "listFiles wiki directory failed:", err);
-    return [];
+    logger.warn("lint", "page-index read failed", err);
   }
 
-  return entries
-    .filter((e) => e.name.endsWith(".md") && !INFRASTRUCTURE_FILES.has(e.name))
-    .map((e) => e.name.replace(/\.md$/, ""));
+  return [];
 }
 
 /**