create-yss-spec 3.5.2 → 3.5.3

package/template/.pi/skills/llm-wiki/scripts/inventory.test.mjs

@@ -1,18 +1,25 @@
 import assert from "node:assert/strict";
 import { spawnSync } from "node:child_process";
-import { mkdir, mkdtemp, writeFile } from "node:fs/promises";
+import { mkdir, mkdtemp, writeFile, readFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import path from "node:path";
 import test from "node:test";
 import { fileURLToPath } from "node:url";
 import { drift, hashSources, sha256, unmappedCandidates } from "./inventory.mjs";
-
 const inventoryCli = fileURLToPath(new URL("./inventory.mjs", import.meta.url));
-
 async function seed() {
   const repo = await mkdtemp(path.join(tmpdir(), "llm-wiki-inv-"));
   const wiki = path.join(repo, "wiki-root");
   await mkdir(path.join(wiki, "raw"), { recursive: true });
+  await mkdir(path.join(wiki, "wiki"));
+  await writeFile(path.join(wiki, "raw/api.md"), "v1\n");
+  for (const id of ["API契约", "人工页"]) await writeFile(path.join(wiki, `wiki/${id}.md`), `# ${id}
+
+Summary.
+
+## 来源
+- api.md
+`);
   const liveRel = "docs/api.md";
   const live = path.join(repo, liveRel);
   await mkdir(path.dirname(live), { recursive: true });
@@ -29,28 +36,31 @@ async function seed() {
           kind: "document",
           livePath: liveRel,
           rawPath: "raw/api.md",
-          sha256: "",
-          role: "copy",
-        },
+          sha256: sha256("v1\n"),
+          role: "copy"
+        }
       ],
       articles: [
         { id: "API契约", file: "wiki/API契约.md", sourceIds: ["api.md"], humanOwned: false },
-        { id: "人工页", file: "wiki/人工页.md", sourceIds: ["api.md"], humanOwned: true },
-      ],
+        { id: "人工页", file: "wiki/人工页.md", sourceIds: ["api.md"], humanOwned: true }
+      ]
     }),
-    "utf8",
+    "utf8"
   );
   return { repo, wiki, live, liveRel };
 }
-
-test("hash-sources fills sha256; drift is empty until live file changes", async () => {
+test("hash-sources only observes; v1 remains unverified until compiled", async () => {
   const { repo, wiki, live } = await seed();
+  const before = await readFile(path.join(wiki, ".wiki-manifest.json"));
   const hashed = await hashSources({ wikiRoot: wiki, repoRoot: repo, now: "2026-01-01T00:00:00Z" });
   assert.equal(hashed.missing.length, 0);
+  assert.deepEqual(await readFile(path.join(wiki, ".wiki-manifest.json")), before);
+  assert.equal(hashed.observations[0].originalDigest, sha256("v1\n"));
   assert.equal(hashed.manifest.sources[0].sha256, sha256(Buffer.from("v1\n")));
   const clean = await drift({ wikiRoot: wiki, repoRoot: repo });
   assert.deepEqual(clean.changed, []);
-  assert.deepEqual(clean.articles, []);
+  assert.deepEqual(clean.articles, ["API契约", "人工页"]);
+  assert.equal(clean.articleStates.every((a) => a.state === "unverified"), true);
   await writeFile(live, "v2\n", "utf8");
   const dirty = await drift({ wikiRoot: wiki, repoRoot: repo });
   assert.deepEqual(dirty.changed, ["api.md"]);
@@ -58,20 +68,18 @@ test("hash-sources fills sha256; drift is empty until live file changes", async
   assert.deepEqual(dirty.humanOwned, ["人工页"]);
   assert.deepEqual(dirty.unmapped, []);
 });
-
 test("unmapped candidates are listed without scanning the tree", () => {
   const sources = [{ livePath: "docs/api.md" }];
   assert.deepEqual(unmappedCandidates(sources, ["docs/api.md", "docs/new.md", "./docs/new.md"]), [
-    "docs/new.md",
+    "docs/new.md"
   ]);
 });
-
 test("drift CLI exits 0 when sources changed and prints JSON", async () => {
   const { repo, wiki, live } = await seed();
   await hashSources({ wikiRoot: wiki, repoRoot: repo, now: "2026-01-01T00:00:00Z" });
   await writeFile(live, "v2\n", "utf8");
   const ran = spawnSync(process.execPath, [inventoryCli, "drift", "--wiki", wiki, "--repo", repo], {
-    encoding: "utf8",
+    encoding: "utf8"
   });
   assert.equal(ran.status, 0, ran.stderr);
   const report = JSON.parse(ran.stdout);
@@ -80,7 +88,6 @@ test("drift CLI exits 0 when sources changed and prints JSON", async () => {
   assert.deepEqual(report.humanOwned, ["人工页"]);
   assert.deepEqual(report.unmapped, []);
 });
-
 test("status CLI exits 0 and lists unmapped candidates", async () => {
   const { repo, wiki, live } = await seed();
   await hashSources({ wikiRoot: wiki, repoRoot: repo, now: "2026-01-01T00:00:00Z" });
@@ -88,7 +95,7 @@ test("status CLI exits 0 and lists unmapped candidates", async () => {
   const ran = spawnSync(
     process.execPath,
     [inventoryCli, "status", "--wiki", wiki, "--repo", repo, "--candidate", "docs/extra.md"],
-    { encoding: "utf8" },
+    { encoding: "utf8" }
   );
   assert.equal(ran.status, 0, ran.stderr);
   const report = JSON.parse(ran.stdout);

package/template/.pi/skills/llm-wiki/scripts/lint-wikilinks.mjs

@@ -2,31 +2,28 @@
 import { readFile, readdir } from "node:fs/promises";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
-import { EXTRACT_KINDS } from "./extract.mjs";
-import { exists, sha256 } from "./inventory.mjs";
-
-export const INFRA = new Set([
+import { exists, safePath, frontmatter, sourceSection, validateManifest, checkPaths, ownership, transactionState, cliError } from "./core.mjs";
+import { drift } from "./inventory.mjs";
+const INFRA = /* @__PURE__ */ new Set([
   "index.md",
   "log.md",
   "claude.md",
   "agents.md",
   "soul.md",
-  "concept-table.md",
+  "concept-table.md"
 ]);
 const WIKILINK_RE = /\[\[([^\]|#]+)(?:[|#][^\]]*)?\]\]/g;
 const SOURCE_HEADING_RE = /^##\s+来源\s*$/m;
 const H1_RE = /^#\s+(.+?)\s*$/m;
-
-export function articlesDir(wikiRoot) {
+function articlesDir(wikiRoot) {
   return path.join(wikiRoot, "wiki");
 }
-
-export function extractLinks(text) {
+function extractLinks(text) {
   const ids = [];
   const invalid = [];
   WIKILINK_RE.lastIndex = 0;
   let match;
-  while ((match = WIKILINK_RE.exec(text))) {
+  while (match = WIKILINK_RE.exec(text)) {
     const target = match[1].trim();
     if (!target) continue;
     if (target.startsWith("../") || target.includes("/")) {
@@ -37,34 +34,61 @@ export function extractLinks(text) {
   }
   return { ids, invalid };
 }
-
-export async function lintWiki(wikiRoot, { repoRoot = process.cwd() } = {}) {
+async function lintWiki(wikiRoot, { repoRoot = process.cwd(), structureOnly = false } = {}) {
+  const errors = [];
+  let manifest;
+  try {
+    const mf = await safePath(wikiRoot, ".wiki-manifest.json");
+    if (await exists(mf)) {
+      manifest = JSON.parse(await readFile(mf, "utf8"));
+      errors.push(...validateManifest(manifest));
+      if (!errors.length) await checkPaths(manifest, { wikiRoot, repoRoot });
+    }
+    await safePath(wikiRoot, "wiki/index.md");
+  } catch (error) {
+    errors.push(error.message);
+  }
+  if (errors.length) {
+    try {
+      const files = await readdir(await safePath(wikiRoot, "wiki"));
+      for (const file of files.filter((f) => f.endsWith(".md") && !INFRA.has(f.toLowerCase())))
+        if (!manifest?.articles?.some((a) => a.file === `wiki/${file}`)) errors.push(`UNLISTED ARTICLE: ${file}`);
+    } catch {
+    }
+    return { ok: false, errors, counts: {} };
+  }
   const dir = articlesDir(wikiRoot);
-  if (!(await exists(path.join(dir, "index.md")))) {
+  if (!await exists(path.join(dir, "index.md"))) {
     return { ok: false, errors: [`missing ${path.join(dir, "index.md")}`], counts: {} };
   }
   const names = (await readdir(dir)).filter((name) => name.endsWith(".md"));
   const articleFiles = names.filter((name) => !INFRA.has(name.toLowerCase()));
   const articleIds = new Set(articleFiles.map((name) => name.slice(0, -3)));
-  const errors = [];
   let linkCount = 0;
-
-  const indexText = await readFile(path.join(dir, "index.md"), "utf8");
+  const indexText = await readFile(await safePath(wikiRoot, "wiki/index.md"), "utf8");
   const indexLinks = extractLinks(indexText);
   linkCount += indexLinks.ids.length;
   for (const target of indexLinks.invalid) errors.push(`CROSS-WIKI (index): [[${target}]]`);
-  const indexed = new Set();
+  const indexed = /* @__PURE__ */ new Set();
   for (const id of indexLinks.ids) {
     indexed.add(id);
     if (!articleIds.has(id)) errors.push(`MISSING (index): [[${id}]]`);
   }
-
   for (const file of articleFiles) {
     const id = file.slice(0, -3);
-    const text = await readFile(path.join(dir, file), "utf8");
+    let text;
+    try {
+      text = await readFile(await safePath(wikiRoot, `wiki/${file}`), "utf8");
+      frontmatter(text);
+    } catch (error) {
+      errors.push(error.message);
+      continue;
+    }
     const heading = text.match(H1_RE);
     if (!heading || heading[1] !== id) errors.push(`H1 MISMATCH: ${file} expected # ${id}`);
-    if (!SOURCE_HEADING_RE.test(text)) errors.push(`NO SOURCE SECTION: ${file}`);
+    if (!sourceSection(text)) errors.push(`NO SOURCE SECTION: ${file}`);
+    const article = manifest?.articles.find((a) => a.id === id);
+    if (article && ownership(article, text).conflict) errors.push(`OWNERSHIP_CONFLICT: ${id}`);
     if (!indexed.has(id)) errors.push(`ORPHAN: ${file}`);
     const links = extractLinks(text);
     for (const target of links.invalid) errors.push(`CROSS-WIKI: ${file} -> [[${target}]]`);
@@ -73,76 +97,25 @@ export async function lintWiki(wikiRoot, { repoRoot = process.cwd() } = {}) {
       if (!articleIds.has(target)) errors.push(`MISSING: ${file} -> [[${target}]]`);
     }
   }
-
-  const manifestFile = path.join(wikiRoot, ".wiki-manifest.json");
-  if (await exists(manifestFile)) {
-    const manifest = JSON.parse(await readFile(manifestFile, "utf8"));
-    const sourceById = new Map();
-    for (const source of manifest.sources || []) {
-      if (source?.id) sourceById.set(source.id, source);
-    }
-    const listedFiles = new Set();
-    for (const article of manifest.articles || []) {
-      const rel = path.posix.normalize(article.file || "");
-      listedFiles.add(rel);
-      const expectedId = path.posix.basename(rel, ".md");
-      if (article.id !== expectedId) {
-        errors.push(`MANIFEST ID MISMATCH: ${article.file} id=${article.id} expected ${expectedId}`);
-      }
-      const file = path.resolve(wikiRoot, article.file);
-      if (!(await exists(file))) errors.push(`MANIFEST ARTICLE MISSING: ${article.file}`);
-      for (const sourceId of article.sourceIds || []) {
-        if (!sourceById.has(sourceId)) {
-          errors.push(`UNKNOWN SOURCE ID: ${article.id} -> ${sourceId}`);
-        }
-      }
-    }
-    for (const file of articleFiles) {
-      const rel = path.posix.join("wiki", file);
-      if (!listedFiles.has(rel)) errors.push(`UNLISTED ARTICLE: ${file}`);
-    }
-    for (const source of manifest.sources || []) {
-      if (manifest.profile === "documents" && source.kind === "code-surface") {
-        errors.push(`PROFILE KIND: documents forbids code-surface (${source.id})`);
-      }
-      if (source.kind === "document" || source.kind === "derived") {
-        if (!source.rawPath) {
-          errors.push(`RAW PATH REQUIRED: ${source.id} (${source.kind})`);
-        } else {
-          const raw = path.resolve(wikiRoot, source.rawPath);
-          if (!(await exists(raw))) errors.push(`RAW MISSING: ${source.id} (${source.rawPath})`);
-        }
-      }
-      if (source.kind === "derived") {
-        const extractKind = source.extract?.kind;
-        if (!extractKind) errors.push(`EXTRACT REQUIRED: ${source.id}`);
-        else if (!EXTRACT_KINDS.includes(extractKind)) {
-          errors.push(`EXTRACT KIND: ${source.id} (${extractKind})`);
-        }
-      }
-      if (source.kind === "code-surface" && source.rawPath != null) {
-        errors.push(`RAW PATH FORBIDDEN: ${source.id} (code-surface)`);
-      }
-      if (!source.livePath) continue;
-      const live = path.resolve(repoRoot, source.livePath);
-      if (!(await exists(live))) {
-        errors.push(`MANIFEST SOURCE MISSING: ${source.id} (${source.livePath})`);
-        continue;
-      }
-      const current = sha256(await readFile(live));
-      if (!source.sha256 || current !== source.sha256) {
-        errors.push(`STALE HASH: ${source.id} (${source.livePath})`);
-      }
+  if (manifest) {
+    const listed = new Set(manifest.articles.map((a) => a.file));
+    for (const file of articleFiles) if (!listed.has(`wiki/${file}`)) errors.push(`UNLISTED ARTICLE: ${file}`);
+    for (const a of manifest.articles) if (!await exists(await safePath(wikiRoot, a.file))) errors.push(`MANIFEST ARTICLE MISSING: ${a.file}`);
+    for (const s of manifest.sources) if (s.rawPath && !await exists(await safePath(wikiRoot, s.rawPath))) errors.push(`RAW MISSING: ${s.id} (${s.rawPath})`);
+    if (!structureOnly) {
+      const report = await drift({ wikiRoot, repoRoot });
+      for (const s of report.sourceStates) if (!["current", "archived"].includes(s.state)) errors.push(`STALE HASH / ${s.state}: ${s.id} (${s.reason})`);
+      for (const a of report.articleStates) if (!["current", "archived"].includes(a.state)) errors.push(`ARTICLE ${a.state}: ${a.id} (${a.reason})`);
     }
   }
-
+  const tx = await transactionState(wikiRoot);
+  if (tx.incomplete || tx.state === "locked") errors.push("TRANSACTION_INCOMPLETE");
   return {
     ok: errors.length === 0,
     errors,
-    counts: { articles: articleFiles.length, links: linkCount },
+    counts: { articles: articleFiles.length, links: linkCount }
   };
 }
-
 async function main(argv = process.argv.slice(2)) {
   let wikiArg;
   let repoRoot = process.cwd();
@@ -155,23 +128,27 @@ async function main(argv = process.argv.slice(2)) {
     throw new Error("usage: lint-wikilinks.mjs <wiki-root> [--repo <repo-root>]");
   }
   const wikiRoot = path.resolve(repoRoot, wikiArg);
-  const result = await lintWiki(wikiRoot, { repoRoot });
-  for (const error of result.errors) process.stdout.write(`${error}\n`);
+  const result = await lintWiki(wikiRoot, { repoRoot, structureOnly: argv.includes("--structure-only") });
+  for (const error of result.errors) process.stdout.write(`${error}
+`);
   process.stdout.write(
-    `校验完成：${result.counts.articles || 0} 篇文章，${result.counts.links || 0} 条 wikilink\n`,
+    `校验完成：${result.counts.articles || 0} 篇文章，${result.counts.links || 0} 条 wikilink
+`
   );
   if (result.ok) process.stdout.write("通过：所有 wikilink / 来源 / 索引检查通过\n");
   else {
     process.stdout.write(
-      "失败：存在缺失的 wikilink、孤儿页、来源小节、跨路径链接、H1 或 manifest 闭合问题\n",
+      "失败：存在缺失的 wikilink、孤儿页、来源小节、跨路径链接、H1 或 manifest 闭合问题\n"
     );
     process.exitCode = 1;
   }
 }
-
 if (process.argv[1] === fileURLToPath(import.meta.url)) {
-  main().catch((error) => {
-    process.stderr.write(`${error.message}\n`);
-    process.exitCode = 2;
-  });
+  main().catch(cliError);
 }
+export {
+  INFRA,
+  articlesDir,
+  extractLinks,
+  lintWiki
+};

package/template/.pi/skills/llm-wiki/scripts/lint-wikilinks.test.mjs

@@ -6,16 +6,13 @@ import test from "node:test";
 import { fileURLToPath } from "node:url";
 import { sha256 } from "./inventory.mjs";
 import { lintWiki } from "./lint-wikilinks.mjs";
-
 const skillRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "..");
 const broken = path.join(skillRoot, "assets/fixtures/broken-wiki");
-
 test("broken fixture fails on dangling wikilink", async () => {
   const result = await lintWiki(broken);
   assert.equal(result.ok, false);
   assert.ok(result.errors.some((line) => line.includes("[[不存在的页]]")));
 });
-
 test("complete wiki passes wikilink, index, and source-section checks", async () => {
   const root = await mkdtemp(path.join(tmpdir(), "llm-wiki-lint-"));
   const wiki = path.join(root, "wiki");
@@ -23,19 +20,18 @@ test("complete wiki passes wikilink, index, and source-section checks", async ()
   await writeFile(
     path.join(wiki, "index.md"),
     "# index\n\n## 分类\n\n- [[Alpha]]\n",
-    "utf8",
+    "utf8"
   );
   await writeFile(
     path.join(wiki, "Alpha.md"),
     "# Alpha\n\nSee [[Alpha]].\n\n## 来源\n\n- live\n",
-    "utf8",
+    "utf8"
   );
   await writeFile(path.join(wiki, "CLAUDE.md"), "# schema\n", "utf8");
   const result = await lintWiki(root);
   assert.equal(result.ok, true, result.errors.join("\n"));
   assert.equal(result.counts.articles, 1);
 });
-
 test("cross-path wikilink fails instead of being ignored", async () => {
   const root = await mkdtemp(path.join(tmpdir(), "llm-wiki-cross-"));
   const wiki = path.join(root, "wiki");
@@ -44,13 +40,12 @@ test("cross-path wikilink fails instead of being ignored", async () => {
   await writeFile(
     path.join(wiki, "Alpha.md"),
     "# Alpha\n\nSee [[../other]]\n\n## 来源\n\n- live\n",
-    "utf8",
+    "utf8"
   );
   const result = await lintWiki(root);
   assert.equal(result.ok, false);
   assert.ok(result.errors.some((line) => line.includes("CROSS-WIKI") && line.includes("[[../other]]")));
 });
-
 test("manifest sha256 mismatch is stale", async () => {
   const repo = await mkdtemp(path.join(tmpdir(), "llm-wiki-hash-"));
   const wikiRoot = path.join(repo, "wiki-root");
@@ -73,18 +68,17 @@ test("manifest sha256 mismatch is stale", async () => {
           kind: "document",
           livePath: liveRel,
           rawPath: "raw/api.md",
-          sha256: sha256(Buffer.from("v1\n")),
-        },
+          sha256: sha256(Buffer.from("v1\n"))
+        }
       ],
-      articles: [{ id: "API", file: "wiki/API.md", sourceIds: ["api.md"] }],
+      articles: [{ id: "API", file: "wiki/API.md", sourceIds: ["api.md"] }]
     }),
-    "utf8",
+    "utf8"
   );
   const result = await lintWiki(wikiRoot, { repoRoot: repo });
   assert.equal(result.ok, false);
   assert.ok(result.errors.some((line) => line.includes("STALE HASH") && line.includes("api.md")));
 });
-
 async function seedClosedWiki() {
   const repo = await mkdtemp(path.join(tmpdir(), "llm-wiki-closed-"));
   const wikiRoot = path.join(repo, "wiki-root");
@@ -99,7 +93,7 @@ async function seedClosedWiki() {
   await writeFile(
     path.join(wiki, "Alpha.md"),
     "# Alpha\n\nSee [[Alpha]].\n\n## 来源\n\n- live\n",
-    "utf8",
+    "utf8"
   );
   const manifest = {
     schemaVersion: 1,
@@ -110,21 +104,19 @@ async function seedClosedWiki() {
         kind: "document",
         livePath: liveRel,
         rawPath: "raw/api.md",
-        sha256: sha256(Buffer.from("v1\n")),
-      },
+        sha256: sha256(Buffer.from("v1\n"))
+      }
     ],
-    articles: [{ id: "Alpha", file: "wiki/Alpha.md", sourceIds: ["api.md"] }],
+    articles: [{ id: "Alpha", file: "wiki/Alpha.md", sourceIds: ["api.md"] }]
   };
   await writeFile(path.join(wikiRoot, ".wiki-manifest.json"), JSON.stringify(manifest), "utf8");
   return { repo, wikiRoot, wiki, manifest };
 }
-
 test("closed manifest passes listing, id, sourceIds, profile, and rawPath checks", async () => {
   const { repo, wikiRoot } = await seedClosedWiki();
-  const result = await lintWiki(wikiRoot, { repoRoot: repo });
+  const result = await lintWiki(wikiRoot, { repoRoot: repo, structureOnly: true });
   assert.equal(result.ok, true, result.errors.join("\n"));
 });
-
 test("open manifest fails unlisted article, id mismatch, unknown source, profile kind, and rawPath", async () => {
   const repo = await mkdtemp(path.join(tmpdir(), "llm-wiki-open-"));
   const wikiRoot = path.join(repo, "wiki-root");
@@ -146,27 +138,27 @@ test("open manifest fails unlisted article, id mismatch, unknown source, profile
           kind: "code-surface",
           livePath: "docs/api.md",
           rawPath: "raw/should-not-exist.md",
-          sha256: sha256(Buffer.from("v1\n")),
+          sha256: sha256(Buffer.from("v1\n"))
         },
         {
           id: "note",
           kind: "document",
           livePath: "docs/api.md",
           rawPath: "",
-          sha256: sha256(Buffer.from("v1\n")),
-        },
+          sha256: sha256(Buffer.from("v1\n"))
+        }
       ],
       articles: [
         {
           id: "WrongId",
           file: "wiki/Alpha.md",
-          sourceIds: ["api.md", "ghost"],
-        },
-      ],
+          sourceIds: ["api.md", "ghost"]
+        }
+      ]
     }),
-    "utf8",
+    "utf8"
   );
-  const result = await lintWiki(wikiRoot, { repoRoot: repo });
+  const result = await lintWiki(wikiRoot, { repoRoot: repo, structureOnly: true });
   assert.equal(result.ok, false);
   assert.ok(result.errors.some((line) => line.includes("UNLISTED ARTICLE") && line.includes("Beta.md")));
   assert.ok(result.errors.some((line) => line.includes("MANIFEST ID MISMATCH") && line.includes("WrongId")));
@@ -175,7 +167,6 @@ test("open manifest fails unlisted article, id mismatch, unknown source, profile
   assert.ok(result.errors.some((line) => line.includes("RAW PATH REQUIRED") && line.includes("note")));
   assert.ok(result.errors.some((line) => line.includes("RAW PATH FORBIDDEN") && line.includes("api.md")));
 });
-
 test("derived source requires a known extract.kind", async () => {
   const { repo, wikiRoot, manifest } = await seedClosedWiki();
   manifest.sources.push({
@@ -183,30 +174,27 @@ test("derived source requires a known extract.kind", async () => {
     kind: "derived",
     livePath: "docs/api.md",
     rawPath: "raw/api.md",
-    sha256: sha256(Buffer.from("v1\n")),
+    sha256: sha256(Buffer.from("v1\n"))
   });
   await writeFile(path.join(wikiRoot, ".wiki-manifest.json"), JSON.stringify(manifest), "utf8");
-  const missing = await lintWiki(wikiRoot, { repoRoot: repo });
+  const missing = await lintWiki(wikiRoot, { repoRoot: repo, structureOnly: true });
   assert.equal(missing.ok, false);
   assert.ok(missing.errors.some((line) => line.includes("EXTRACT REQUIRED") && line.includes("lock")));
-
   manifest.sources.at(-1).extract = { kind: "whole-file" };
   await writeFile(path.join(wikiRoot, ".wiki-manifest.json"), JSON.stringify(manifest), "utf8");
-  const unknown = await lintWiki(wikiRoot, { repoRoot: repo });
+  const unknown = await lintWiki(wikiRoot, { repoRoot: repo, structureOnly: true });
   assert.equal(unknown.ok, false);
   assert.ok(unknown.errors.some((line) => line.includes("EXTRACT KIND") && line.includes("whole-file")));
-
   manifest.sources.at(-1).extract = { kind: "skill-names" };
   await writeFile(path.join(wikiRoot, ".wiki-manifest.json"), JSON.stringify(manifest), "utf8");
-  const ok = await lintWiki(wikiRoot, { repoRoot: repo });
+  const ok = await lintWiki(wikiRoot, { repoRoot: repo, structureOnly: true });
   assert.equal(ok.ok, true, ok.errors.join("\n"));
 });
-
 test("document rawPath must exist on disk", async () => {
   const { repo, wikiRoot, manifest } = await seedClosedWiki();
   manifest.sources[0].rawPath = "raw/missing.md";
   await writeFile(path.join(wikiRoot, ".wiki-manifest.json"), JSON.stringify(manifest), "utf8");
-  const result = await lintWiki(wikiRoot, { repoRoot: repo });
+  const result = await lintWiki(wikiRoot, { repoRoot: repo, structureOnly: true });
   assert.equal(result.ok, false);
   assert.ok(result.errors.some((line) => line.includes("RAW MISSING") && line.includes("raw/missing.md")));
 });

package/template/.pi/skills/llm-wiki/scripts/migrate.mjs

@@ -0,0 +1,51 @@
+#!/usr/bin/env node
+import { readFile } from "node:fs/promises";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import { loadManifest, safePath, digestFile, sha256, json, ownership, fail, args, cliError } from "./core.mjs";
+import { createPlan, applyPlan } from "./transaction.mjs";
+async function migrate({ wikiRoot, repoRoot = process.cwd(), apply = false }) {
+  const prior = await loadManifest(wikiRoot, { repoRoot });
+  if (prior.schemaVersion === 2) return { schemaVersion: 2, changed: false, readOnly: !apply };
+  const original = await readFile(await safePath(wikiRoot, ".wiki-manifest.json"), "utf8");
+  const manifest = structuredClone(prior);
+  manifest.schemaVersion = 2;
+  manifest.profile ||= "mixed";
+  manifest.feedback = [];
+  for (const s of manifest.sources) {
+    s.originalDigest = s.sha256 || null;
+    s.effectiveDigest = s.kind === "derived" ? null : s.sha256 || null;
+    s.rawDigest = s.rawPath ? await digestFile(await safePath(wikiRoot, s.rawPath)) : null;
+    s.location = s.livePath || s.url || `snapshot:${s.rawPath}`;
+    if (s.kind === "derived") {
+      s.extract = { ...s.extract, version: "1", inputs: s.extract?.inputs || [s.livePath].filter(Boolean) };
+      if (s.extract.kind === "prose-note") {
+        s.extract.inputDigests = {};
+        s.extract.rules ||= "legacy-unknown; explicit recipe required before recompilation";
+      }
+    }
+  }
+  for (const a of manifest.articles) {
+    a.articleDigest = null;
+    a.compiledFrom = {};
+    a.compiledDependencies = {};
+    a.verification = null;
+    a.dependsOnArticles ||= [];
+    a.aliases ||= [];
+    const text = await readFile(await safePath(wikiRoot, a.file), "utf8");
+    a.humanOwned = ownership(a, text).protected;
+  }
+  const backup = `.wiki-backups/manifest-v1-${sha256(original)}.json`;
+  const plan = await createPlan({ wikiRoot, repoRoot, request: { operation: "migrate", manifest, writes: [{ path: backup, content: original }], authorization: { confirmed: true, paths: [backup, ".wiki-manifest.json", "wiki/log.md"] } } });
+  if (!apply) return { changed: true, readOnly: true, backup, plan };
+  return { ...await applyPlan({ wikiRoot, repoRoot, plan }), changed: true, backup, remaining: "unverified; migration does not compile articles" };
+}
+async function main() {
+  const a = args(process.argv.slice(2));
+  if (!a.wiki) fail("USAGE", "migrate.mjs --wiki <root> [--repo <root>] [--apply]");
+  process.stdout.write(json(await migrate({ wikiRoot: path.resolve(a.repo, a.wiki), repoRoot: path.resolve(a.repo), apply: a.apply === true })));
+}
+if (process.argv[1] === fileURLToPath(import.meta.url)) main().catch(cliError);
+export {
+  migrate
+};