skillwiki 0.2.0-beta.26 → 0.2.0-beta.28

package/dist/cli.js

@@ -4,7 +4,7 @@ import {
 } from "./chunk-XM5IYZX7.js";
 
 // src/cli.ts
-import { readFileSync as readFileSync4 } from "fs";
+import { readFileSync as readFileSync5 } from "fs";
 import { Command } from "commander";
 
 // src/utils/output.ts
@@ -72,7 +72,8 @@ var ExitCode = {
   DRIFT_DETECTED: 32,
   RAW_DEDUP_DETECTED: 33,
   MIGRATION_APPLIED: 34,
-  UNKNOWN_WIKI_PROFILE: 35
+  UNKNOWN_WIKI_PROFILE: 35,
+  DEDUP_APPLIED: 36
 };
 
 // ../shared/src/json-output.ts
@@ -796,6 +797,9 @@ var MARKER_RE = /\^\[(raw\/[^\]]+)\]/g;
 function stripFences(body) {
   return body.replace(FENCE2, "").replace(INLINE_CODE, "");
 }
+function stripFencedBlocks(body) {
+  return body.replace(FENCE2, "");
+}
 function extractCitationMarkers(body) {
   const stripped = stripFences(body);
   const out = [];
@@ -806,7 +810,7 @@ function extractCitationMarkers(body) {
   return out;
 }
 function hasSourcesFooter(body) {
-  return /^## Sources\s*$/m.test(stripFences(body));
+  return /^## Sources\s*$/m.test(stripFencedBlocks(body));
 }
 function isLegacyCitationStyle(body) {
   const markers = extractCitationMarkers(body);
@@ -898,7 +902,7 @@ async function runAudit(input) {
       return { ...m, resolved: false };
     }
   }));
-  const sources = fm.data.sources ?? [];
+  const sources = (fm.data.sources ?? []).map((s) => s.replace(/^\^\[/, "").replace(/\]$/, ""));
   const referenced = new Set(resolved.map((m) => m.target));
   const unused_sources = sources.filter((s) => !referenced.has(s));
   const missing_from_sources = [...referenced].filter((t) => !sources.includes(t));
@@ -1303,8 +1307,7 @@ async function runInit(input) {
     return tpl.replace(/\{\{INIT_DATE\}\}/g, today).replace("{{DOMAIN}}", domain).replace("{{WIKI_LANG}}", canonicalLang);
   });
   if (err22) return err22;
-  const isTempPath = target.startsWith("/tmp/") || target === "/tmp" || target.startsWith("/var/tmp/") || target === "/var/tmp" || target.startsWith("/private/tmp/");
-  const skipEnv = !!input.noEnv || isTempPath;
+  const skipEnv = !!input.noEnv;
   let envWritten = "";
   if (!skipEnv) {
     try {
@@ -1600,6 +1603,8 @@ ${markdown_links.map((l) => `  line ${l.line}: ${l.text}`).join("\n")}`;
 }
 
 // src/commands/dedup.ts
+import { readFileSync, writeFileSync, unlinkSync } from "fs";
+import { join as join13 } from "path";
 async function runDedup(input) {
   const scan = await scanVault(input.vault);
   if (!scan.ok) return { exitCode: ExitCode.VAULT_PATH_INVALID, result: scan };
@@ -1616,17 +1621,63 @@ async function runDedup(input) {
     else hashMap.set(sha, [raw.relPath]);
   }
   const duplicates = [...hashMap.entries()].filter(([, files]) => files.length > 1).map(([sha256, files]) => ({ sha256, files }));
-  const exitCode = duplicates.length > 0 ? ExitCode.RAW_DEDUP_DETECTED : ExitCode.OK;
+  const rewired = [];
+  const removed = [];
+  if (input.apply && duplicates.length > 0) {
+    const replacements = /* @__PURE__ */ new Map();
+    for (const group of duplicates) {
+      const canonical = group.files[0];
+      for (let i = 1; i < group.files.length; i++) {
+        replacements.set(group.files[i], canonical);
+      }
+    }
+    for (const page of scan.data.typedKnowledge) {
+      const text = readFileSync(join13(input.vault, page.relPath), "utf-8");
+      let updated = text;
+      let changed = false;
+      for (const [oldPath, newPath] of replacements) {
+        const oldMarker = `^[${oldPath}]`;
+        const newMarker = `^[${newPath}]`;
+        if (updated.includes(oldMarker)) {
+          updated = updated.replaceAll(oldMarker, newMarker);
+          changed = true;
+        }
+        const oldFm = `- "^[${oldPath}]"`;
+        const newFm = `- "^[${newPath}]"`;
+        if (updated.includes(oldFm)) {
+          updated = updated.replaceAll(oldFm, newFm);
+          changed = true;
+        }
+      }
+      if (changed) {
+        writeFileSync(join13(input.vault, page.relPath), updated);
+        rewired.push(page.relPath);
+      }
+    }
+    for (const [oldPath] of replacements) {
+      const fullPath = join13(input.vault, oldPath);
+      try {
+        unlinkSync(fullPath);
+        removed.push(oldPath);
+      } catch {
+      }
+    }
+  }
+  const exitCode = duplicates.length > 0 ? input.apply ? ExitCode.DEDUP_APPLIED : ExitCode.RAW_DEDUP_DETECTED : ExitCode.OK;
   const hintLines = [`scanned: ${totalFiles} raw files`];
   if (duplicates.length > 0) {
     hintLines.push(`duplicates: ${duplicates.length}`);
     for (const d of duplicates) hintLines.push(`  ${d.sha256.slice(0, 12)}... \u2192 ${d.files.join(", ")}`);
+    if (input.apply) {
+      hintLines.push(`rewired: ${rewired.length} pages`);
+      hintLines.push(`removed: ${removed.length} raw files`);
+    }
   } else {
     hintLines.push("0 duplicates");
   }
   return {
     exitCode,
-    result: ok({ scanned: totalFiles, duplicates, humanHint: hintLines.join("\n") })
+    result: ok({ scanned: totalFiles, duplicates, rewired, removed, humanHint: hintLines.join("\n") })
   };
 }
 
@@ -1645,8 +1696,8 @@ function hasDuplicateFrontmatter(body) {
   return false;
 }
 var ERROR_ORDER = ["broken_wikilinks", "invalid_frontmatter", "raw_dedup", "tag_not_in_taxonomy"];
-var WARNING_ORDER = ["index_incomplete", "index_link_format", "stale_page", "page_too_large", "log_rotate_needed", "contested", "orphans", "legacy_citation_style", "orphaned_citations", "duplicate_frontmatter", "missing_overview"];
-var INFO_ORDER = ["bridges", "low_confidence_single_source", "page_structure", "topic_map_recommended"];
+var WARNING_ORDER = ["index_incomplete", "index_link_format", "stale_page", "page_too_large", "log_rotate_needed", "orphans", "legacy_citation_style", "orphaned_citations", "duplicate_frontmatter", "missing_overview"];
+var INFO_ORDER = ["bridges", "page_structure", "topic_map_recommended", "frontmatter_wikilink"];
 async function runLint(input) {
   const buckets = {};
   const links = await runLinks({ vault: input.vault });
@@ -1690,20 +1741,31 @@ async function runLint(input) {
   const dedup = await runDedup({ vault: input.vault });
   if (dedup.result.ok && dedup.result.data.duplicates.length > 0) buckets.raw_dedup = dedup.result.data.duplicates;
   const scan = await scanVault(input.vault);
+  const slugs = scan.ok ? buildSlugMap(scan.data.typedKnowledge) : /* @__PURE__ */ new Map();
   if (scan.ok) {
     const legacyPages = [];
     const orphanedPages = [];
     const structFlags = [];
     const dupFrontmatter = [];
     const noOverview = [];
+    const fmWikilinkFlags = [];
     for (const page of scan.data.typedKnowledge) {
       const text = await readPage(page);
       const split = splitFrontmatter(text);
       if (!split.ok) continue;
       const body = split.data.body;
+      const rawFm = split.data.rawFrontmatter;
       if (hasDuplicateFrontmatter(body)) dupFrontmatter.push(page.relPath);
       if (isLegacyCitationStyle(body)) legacyPages.push(page.relPath);
       if (hasOrphanedCitations(body)) orphanedPages.push(page.relPath);
+      const fmLinks = rawFm.match(/\[\[([^\[\]|]+)(?:\|[^\[\]]*)?\]\]/g) ?? [];
+      for (const link of fmLinks) {
+        const target = link.replace(/^\[\[/, "").replace(/(?:\|[^\[\]]*)?\]\]$/, "").trim();
+        const tail = target.split("/").pop();
+        if (!slugs.has(tail.toLowerCase())) {
+          fmWikilinkFlags.push(`${page.relPath}: [[${target}]] does not resolve`);
+        }
+      }
       const bodyLines = body.split("\n").filter((l) => l.trim().length > 0).length;
       const hasOverview = /^## Overview/m.test(body);
       if (!hasOverview) noOverview.push(page.relPath);
@@ -1723,6 +1785,7 @@ async function runLint(input) {
     if (structFlags.length > 0) buckets.page_structure = structFlags;
     if (dupFrontmatter.length > 0) buckets.duplicate_frontmatter = dupFrontmatter;
     if (noOverview.length > 0) buckets.missing_overview = noOverview;
+    if (fmWikilinkFlags.length > 0) buckets.frontmatter_wikilink = fmWikilinkFlags;
   }
   const errorOut = ERROR_ORDER.flatMap((k) => buckets[k] ? [{ kind: k, items: buckets[k] }] : []);
   const warningOut = WARNING_ORDER.flatMap((k) => buckets[k] ? [{ kind: k, items: buckets[k] }] : []);
@@ -1758,12 +1821,12 @@ async function runLint(input) {
 // src/commands/config.ts
 import { readFile as readFile12 } from "fs/promises";
 import { existsSync } from "fs";
-import { join as join13 } from "path";
+import { join as join14 } from "path";
 function validateKey(key) {
   return CONFIG_KEYS.includes(key) || isValidWikiProfileKey(key);
 }
 function configPath(home) {
-  return join13(home, ".skillwiki", ".env");
+  return join14(home, ".skillwiki", ".env");
 }
 async function runConfigGet(input) {
   if (!validateKey(input.key)) {
@@ -1817,13 +1880,13 @@ async function runConfigPath(input) {
 }
 
 // src/commands/doctor.ts
-import { existsSync as existsSync3, readdirSync, readFileSync as readFileSync2, statSync } from "fs";
-import { join as join15 } from "path";
+import { existsSync as existsSync3, readdirSync, readFileSync as readFileSync3, statSync } from "fs";
+import { join as join16 } from "path";
 import { execSync } from "child_process";
 
 // src/utils/auto-update.ts
-import { readFileSync, writeFileSync, existsSync as existsSync2, mkdirSync } from "fs";
-import { join as join14, dirname as dirname6 } from "path";
+import { readFileSync as readFileSync2, writeFileSync as writeFileSync2, existsSync as existsSync2, mkdirSync } from "fs";
+import { join as join15, dirname as dirname6 } from "path";
 import { spawn } from "child_process";
 
 // src/utils/update-consts.ts
@@ -1834,11 +1897,11 @@ var CLI_DISABLE_FLAG = "--no-update-notifier";
 
 // src/utils/auto-update.ts
 function cachePath(home) {
-  return join14(home, ".skillwiki", CACHE_FILENAME);
+  return join15(home, ".skillwiki", CACHE_FILENAME);
 }
 function readCacheRaw(home) {
   try {
-    const raw = readFileSync(cachePath(home), "utf8");
+    const raw = readFileSync2(cachePath(home), "utf8");
     return JSON.parse(raw);
   } catch {
     return null;
@@ -1854,7 +1917,7 @@ function readCache(home) {
 function writeCache(home, cache) {
   const p = cachePath(home);
   mkdirSync(dirname6(p), { recursive: true });
-  writeFileSync(p, JSON.stringify(cache, null, 2));
+  writeFileSync2(p, JSON.stringify(cache, null, 2));
 }
 function latestFromCache(home, currentVersion) {
   const { cache } = readCache(home);
@@ -1937,9 +2000,9 @@ function checkVaultStructure(resolvedPath) {
     return check("error", "vault_structure", "Vault structure valid", "Cannot check \u2014 vault directory does not exist");
   }
   const missing = [];
-  if (!existsSync3(join15(resolvedPath, "SCHEMA.md"))) missing.push("SCHEMA.md");
+  if (!existsSync3(join16(resolvedPath, "SCHEMA.md"))) missing.push("SCHEMA.md");
   for (const dir of ["raw", "entities", "concepts", "meta"]) {
-    if (!existsSync3(join15(resolvedPath, dir))) missing.push(dir + "/");
+    if (!existsSync3(join16(resolvedPath, dir))) missing.push(dir + "/");
   }
   if (missing.length === 0) {
     return check("pass", "vault_structure", "Vault structure valid", "All required files and directories present");
@@ -1947,7 +2010,7 @@ function checkVaultStructure(resolvedPath) {
   return check("error", "vault_structure", "Vault structure valid", `Missing: ${missing.join(", ")}`);
 }
 function checkSkillsInstalled(home) {
-  const skillsDir = join15(home, ".claude", "skills");
+  const skillsDir = join16(home, ".claude", "skills");
   if (!existsSync3(skillsDir)) {
     return check("warn", "skills_installed", "Skills installed", `${skillsDir} not found`);
   }
@@ -1968,12 +2031,12 @@ function checkNpmUpdate(home, currentVersion) {
   return check("pass", "npm_update", "npm CLI version", `v${currentVersion} (latest: v${latest})`);
 }
 function checkPluginVersionDrift(home, currentVersion) {
-  const pluginJsonPath = join15(home, ".claude", "plugins", "cache", "llm-wiki", "plugin.json");
+  const pluginJsonPath = join16(home, ".claude", "plugins", "cache", "llm-wiki", "plugin.json");
   if (!existsSync3(pluginJsonPath)) {
     return check("pass", "plugin_version_drift", "Plugin/CLI version", "Plugin cache not found \u2014 plugin not installed");
   }
   try {
-    const content = readFileSync2(pluginJsonPath, { encoding: "utf8" });
+    const content = readFileSync3(pluginJsonPath, { encoding: "utf8" });
     const pluginData = JSON.parse(content);
     const pluginVersion = pluginData.version;
     if (!pluginVersion) {
@@ -2015,7 +2078,7 @@ async function checkProfiles(home) {
 }
 async function checkProjectLocalOverride(cwd) {
   const dir = cwd ?? process.cwd();
-  const envPath = join15(dir, ".skillwiki", ".env");
+  const envPath = join16(dir, ".skillwiki", ".env");
   if (existsSync3(envPath)) {
     return check("pass", "project_local", "Project-local config", `Found: ${envPath}`);
   }
@@ -2031,9 +2094,9 @@ function findSkillMd(dir) {
   }
   for (const entry of entries) {
     if (entry.isFile() && entry.name === "SKILL.md") {
-      results.push(join15(dir, entry.name));
+      results.push(join16(dir, entry.name));
     } else if (entry.isDirectory()) {
-      results.push(...findSkillMd(join15(dir, entry.name)));
+      results.push(...findSkillMd(join16(dir, entry.name)));
     }
   }
   return results;
@@ -2077,7 +2140,7 @@ async function runDoctor(input) {
 
 // src/commands/archive.ts
 import { rename as rename3, mkdir as mkdir5, readFile as readFile13, writeFile as writeFile6 } from "fs/promises";
-import { join as join16, dirname as dirname7 } from "path";
+import { join as join17, dirname as dirname7 } from "path";
 async function runArchive(input) {
   const scan = await scanVault(input.vault);
   if (!scan.ok) return { exitCode: ExitCode.VAULT_PATH_INVALID, result: scan };
@@ -2089,10 +2152,10 @@ async function runArchive(input) {
   }
   if (!relPath) return { exitCode: ExitCode.ARCHIVE_TARGET_NOT_FOUND, result: err("ARCHIVE_TARGET_NOT_FOUND", { page: input.page }) };
   if (relPath.startsWith("_archive/")) return { exitCode: ExitCode.ARCHIVE_ALREADY_ARCHIVED, result: err("ARCHIVE_ALREADY_ARCHIVED", { page: relPath }) };
-  const archivePath = join16("_archive", relPath);
-  await mkdir5(dirname7(join16(input.vault, archivePath)), { recursive: true });
+  const archivePath = join17("_archive", relPath);
+  await mkdir5(dirname7(join17(input.vault, archivePath)), { recursive: true });
   let indexUpdated = false;
-  const indexPath = join16(input.vault, "index.md");
+  const indexPath = join17(input.vault, "index.md");
   try {
     const idx = await readFile13(indexPath, "utf8");
     const slug = relPath.replace(/\.md$/, "").split("/").pop();
@@ -2105,7 +2168,7 @@ async function runArchive(input) {
   } catch (e) {
     if (e?.code !== "ENOENT") throw e;
   }
-  await rename3(join16(input.vault, relPath), join16(input.vault, archivePath));
+  await rename3(join17(input.vault, relPath), join17(input.vault, archivePath));
   return { exitCode: ExitCode.OK, result: ok({ archived_from: relPath, archived_to: archivePath, index_updated: indexUpdated, humanHint: `${relPath} -> ${archivePath}${indexUpdated ? " (index updated)" : ""}` }) };
 }
 
@@ -2404,10 +2467,10 @@ ${newBody}`;
 
 // src/commands/update.ts
 import { execSync as execSync2 } from "child_process";
-import { readFileSync as readFileSync3 } from "fs";
+import { readFileSync as readFileSync4 } from "fs";
 async function runUpdate(input) {
   const pkg2 = JSON.parse(
-    readFileSync3(new URL("../../package.json", import.meta.url), "utf8")
+    readFileSync4(new URL("../../package.json", import.meta.url), "utf8")
   );
   const currentVersion = pkg2.version;
   const tag = input.distTag ?? "beta";
@@ -2464,7 +2527,7 @@ async function runUpdate(input) {
 }
 
 // src/cli.ts
-var pkg = JSON.parse(readFileSync4(new URL("../package.json", import.meta.url), "utf8"));
+var pkg = JSON.parse(readFileSync5(new URL("../package.json", import.meta.url), "utf8"));
 var program = new Command();
 program.name("skillwiki").description("Deterministic helpers for CodeWiki skills").version(pkg.version);
 program.option("--human", "render terminal-readable output instead of JSON");
@@ -2603,10 +2666,10 @@ program.command("drift [vault]").description("detect content drift in raw source
   if (!v.ok) emit({ exitCode: v.exitCode, result: v.payload });
   else emit(await runDrift({ vault: v.vault }));
 });
-program.command("dedup [vault]").description("detect duplicate raw sources by sha256").option("--wiki <name>", "wiki profile name").action(async (vault, opts) => {
+program.command("dedup [vault]").description("detect duplicate raw sources by sha256").option("--apply", "rewire citations and remove duplicate raw files", false).option("--wiki <name>", "wiki profile name").action(async (vault, opts) => {
   const v = await resolveVaultArg(vault, opts.wiki);
   if (!v.ok) emit({ exitCode: v.exitCode, result: v.payload });
-  else emit(await runDedup({ vault: v.vault }));
+  else emit(await runDedup({ vault: v.vault, apply: opts.apply }));
 });
 program.command("migrate-citations [vault]").description("migrate ^[raw/...] markers to paragraph-end citations").option("--dry-run", "preview changes without writing", false).option("--wiki <name>", "wiki profile name").action(async (vault, opts) => {
   const v = await resolveVaultArg(vault, opts.wiki);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "skillwiki",
-  "version": "0.2.0-beta.26",
+  "version": "0.2.0-beta.28",
   "type": "module",
   "bin": {
     "skillwiki": "dist/cli.js"

package/skills/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "skillwiki",
-  "version": "0.2.0-beta.26",
+  "version": "0.2.0-beta.28",
   "skills": "./",
   "description": "Project-aware Karpathy-style knowledge base for Claude Code: 11 prompt-only skills (wiki-*, proj-*, using-skillwiki) backed by the deterministic `skillwiki` CLI (8 subcommands, JSON-by-default).",
   "author": {

package/skills/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@skillwiki/skills",
-  "version": "0.2.0-beta.26",
+  "version": "0.2.0-beta.28",
   "private": true,
   "files": [
     "wiki-*",

package/skills/wiki-archive/SKILL.md

@@ -24,7 +24,8 @@ Standard four reads (SCHEMA, index, log, project context if applicable).
 1. Identify the target page. Confirm with the user which page to archive (show full relPath).
 2. Run `skillwiki archive <page> [vault]`. Read the JSON output.
 3. Verify with `skillwiki index-check [vault]` — confirm no ghost entries remain.
-4. Append a `log.md` entry: `## [{date}] archive | {relPath} → _archive/{subdir}/`.
+4. Run `skillwiki lint [vault]` — check for broken wikilinks from other pages that still reference the archived page. If found, update those pages to point to the replacement or remove the stale link.
+5. Append a `log.md` entry: `## [{date}] archive | {relPath} → _archive/{subdir}/`.
 
 ## Reversibility
 

package/skills/wiki-lint/SKILL.md

@@ -18,7 +18,7 @@ Standard four reads.
 
 0. Resolve vault: `skillwiki path` (record source for context).
 1. Run `skillwiki lint <vault>`. Read the JSON.
-2. Reason over findings; present grouped by severity with concrete suggested actions per kind.
+2. Reason over findings; present grouped by severity with concrete suggested actions per kind. If the CLI was recently updated with new lint checks, re-running lint on the full vault may flag pre-existing pages that predate the new rule — treat these as legitimate findings, not false positives.
 3. If `log_rotate_needed` is present and the user consents, run `skillwiki log-rotate <vault> --apply`. Otherwise leave alone.
 4. Append one `log.md` entry summarizing the lint counts (errors/warnings/info).