@onebrain-ai/cli 2.1.10 → 2.1.12

package/README.md

@@ -111,20 +111,20 @@ The agent reaches outward FROM the vault to every surface where the work actuall
 
 ---
 
-## The Path to Co-Evolution
+## Every Session Sharpens Both
 
-A tightening 3-step loop that sharpens with every cycle.
+OneBrain runs as a tight 3-step loop. Each cycle, both sides sharpen.
 
 <p align="center">
   <picture>
     <source media="(prefers-color-scheme: dark)" srcset="assets/diagrams/coevo-loop-dark.svg">
-    <img alt="Co-Evolution loop — three nodes (01 INITIATE at top, 02 CAPTURE_INTENT at bottom-right, 03 MUTUAL_EVOLUTION at bottom-left) connected by curved arrows flowing clockwise" src="assets/diagrams/coevo-loop-light.svg" width="540">
+    <img alt="Co-Evolution loop — three nodes (01 CAPTURE at top, 02 EVOLVE at bottom-right, 03 WRAPUP at bottom-left) connected by curved arrows flowing clockwise" src="assets/diagrams/coevo-loop-light.svg" width="540">
   </picture>
 </p>
 
-1. **Initiate** — Install the CLI, run `/onboarding`. The agent learns your name, vault, and identity. → `npm install -g @onebrain-ai/cli`
-2. **Capture intent** — Talk in natural language. The agent writes, classifies, and links in real time. → `/braindump` · `/capture` · `/bookmark`
-3. **Mutual evolution** — `/research` and `/distill` expand your knowledge. `/learn` deepens the agent. The loop tightens. → `/research` · `/distill` · `/learn`
+1. **Capture** — Talk to the agent in natural language. It writes, classifies, and links your thoughts in real time. → `/braindump` · `/capture` · `/bookmark`
+2. **Evolve** — `/research` and `/distill` expand your knowledge. `/learn` deepens the agent. The loop tightens. → `/research` · `/distill` · `/learn`
+3. **Wrapup** — `/wrapup` consolidates the session log. `/recap` promotes lessons to memory. → `/wrapup` · `/recap`
 
 ### Behind the loop
 

package/dist/onebrain

@@ -9268,6 +9268,10 @@ async function checkVaultYmlKeys(vaultRoot) {
     if (raw[key] === undefined)
       errors.push(`missing key: ${key}`);
   }
+  for (const key of SOFT_REQUIRED_VAULT_YML_KEYS) {
+    if (raw[key] === undefined)
+      warnings.push(`missing key: ${key}`);
+  }
   const folders = raw["folders"] ?? {};
   for (const key of REQUIRED_FOLDER_KEYS) {
     if (folders[key] === undefined)
@@ -9305,8 +9309,16 @@ async function checkVaultYmlKeys(vaultRoot) {
     };
   }
   if (warnings.length > 0) {
-    const fixableWarnings = warnings.filter((w) => w.includes("onebrain_version") || w.includes("method") || w.includes("runtime.harness"));
-    const hint = fixableWarnings.length > 0 ? "Run onebrain doctor --fix to remove deprecated keys" : undefined;
+    const hasDeprecated = warnings.some((w) => w.includes("onebrain_version") || w.includes("method") || w.includes("runtime.harness"));
+    const hasMissingSoftKey = warnings.some((w) => w.startsWith("missing key:"));
+    let hint;
+    if (hasMissingSoftKey && hasDeprecated) {
+      hint = "Run onebrain doctor --fix to repair vault.yml";
+    } else if (hasMissingSoftKey) {
+      hint = "Run onebrain doctor --fix to backfill defaults";
+    } else if (hasDeprecated) {
+      hint = "Run onebrain doctor --fix to remove deprecated keys";
+    }
     return {
       check: "vault.yml-keys",
       status: "warn",
@@ -9321,6 +9333,39 @@ async function checkVaultYmlKeys(vaultRoot) {
     message: "schema ok"
   };
 }
+async function checkClaudeSettings(vaultRoot) {
+  const settingsPath = join2(vaultRoot, ".claude", "settings.json");
+  const file = Bun.file(settingsPath);
+  if (!await file.exists()) {
+    return { check: "claude-settings", status: "ok", message: "no vault settings.json" };
+  }
+  let raw;
+  try {
+    raw = JSON.parse(await file.text());
+  } catch {
+    return {
+      check: "claude-settings",
+      status: "warn",
+      message: "settings.json contains invalid JSON"
+    };
+  }
+  const marketplaces = raw["extraKnownMarketplaces"];
+  const onebrain = marketplaces?.["onebrain"];
+  const source = onebrain?.["source"];
+  const repo = source?.["repo"];
+  if (repo === STALE_MARKETPLACE_REPO) {
+    return {
+      check: "claude-settings",
+      status: "warn",
+      message: "stale marketplace repo",
+      hint: "Run onebrain doctor --fix to rewrite to onebrain-ai/onebrain",
+      details: [
+        `stale extraKnownMarketplaces.onebrain.source.repo: ${STALE_MARKETPLACE_REPO} \u2192 ${CANONICAL_MARKETPLACE_REPO}`
+      ]
+    };
+  }
+  return { check: "claude-settings", status: "ok", message: "ok" };
+}
 function hookPresent(settings, event, cmdSubstring) {
   const groups = settings.hooks?.[event] ?? [];
   return groups.some((g) => g.hooks?.some((h) => (h.command ?? "").includes(cmdSubstring)));
@@ -9407,7 +9452,7 @@ async function checkSettingsHooks(vaultRoot, config) {
     ...okDetails.length > 0 ? { details: okDetails } : {}
   };
 }
-var import_yaml2, STANDARD_FOLDER_KEYS, REQUIRED_PLUGIN_FILES, REQUIRED_PLUGIN_DIRS, STALE_BASH_FILES, REQUIRED_VAULT_YML_KEYS, REQUIRED_FOLDER_KEYS, REQUIRED_HOOKS, ALLOWED_HOOK_EVENTS, QMD_HOOK_SUBSTRING = "onebrain qmd-reindex", ONEBRAIN_COMMAND_SUBSTRING = "onebrain", REQUIRED_PERMISSION = "Bash(onebrain *)", STALE_HOOK_SUBSTRINGS;
+var import_yaml2, STANDARD_FOLDER_KEYS, REQUIRED_PLUGIN_FILES, REQUIRED_PLUGIN_DIRS, STALE_BASH_FILES, REQUIRED_VAULT_YML_KEYS, SOFT_REQUIRED_VAULT_YML_KEYS, REQUIRED_FOLDER_KEYS, STALE_MARKETPLACE_REPO = "kengio/onebrain", CANONICAL_MARKETPLACE_REPO = "onebrain-ai/onebrain", REQUIRED_HOOKS, ALLOWED_HOOK_EVENTS, QMD_HOOK_SUBSTRING = "onebrain qmd-reindex", ONEBRAIN_COMMAND_SUBSTRING = "onebrain", REQUIRED_PERMISSION = "Bash(onebrain *)", STALE_HOOK_SUBSTRINGS;
 var init_validator = __esm(() => {
   import_yaml2 = __toESM(require_dist(), 1);
   STANDARD_FOLDER_KEYS = [
@@ -9431,7 +9476,8 @@ var init_validator = __esm(() => {
     "qmd-reindex.sh",
     "backfill-recapped.sh"
   ];
-  REQUIRED_VAULT_YML_KEYS = ["update_channel", "folders"];
+  REQUIRED_VAULT_YML_KEYS = ["folders"];
+  SOFT_REQUIRED_VAULT_YML_KEYS = ["update_channel"];
   REQUIRED_FOLDER_KEYS = [
     "inbox",
     "projects",
@@ -9449,17 +9495,33 @@ var init_validator = __esm(() => {
   STALE_HOOK_SUBSTRINGS = ["checkpoint-hook.sh", "session-init.sh"];
 });
 
+// src/lib/fs-atomic.ts
+import { rename, unlink, writeFile } from "fs/promises";
+async function atomicWrite(dest, contents, label) {
+  const tmpPath = `${dest}.tmp`;
+  await writeFile(tmpPath, contents, "utf8");
+  try {
+    await rename(tmpPath, dest);
+  } catch (err) {
+    await unlink(tmpPath).catch(() => {});
+    const msg = err instanceof Error ? err.message : String(err);
+    throw new Error(`rename failed for ${label ?? dest}; tmp cleaned up: ${msg}`, { cause: err });
+  }
+}
+var init_fs_atomic = () => {};
+
 // src/lib/index.ts
 var init_lib = __esm(() => {
   init_parser();
   init_validator();
+  init_fs_atomic();
 });
 
 // package.json
 var require_package = __commonJS((exports, module) => {
   module.exports = {
     name: "@onebrain-ai/cli",
-    version: "2.1.10",
+    version: "2.1.12",
     description: "CLI for OneBrain \u2014 personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
     keywords: [
       "onebrain",
@@ -9940,7 +10002,7 @@ __export(exports_register_hooks, {
   runRegisterHooks: () => runRegisterHooks,
   registerHooksCommand: () => registerHooksCommand
 });
-import { mkdir, readFile, rename, writeFile } from "fs/promises";
+import { mkdir, readFile, rename as rename2, writeFile as writeFile2 } from "fs/promises";
 import { homedir } from "os";
 import { dirname, join as join4 } from "path";
 async function readSettings(settingsPath) {
@@ -9956,8 +10018,8 @@ async function readSettings(settingsPath) {
 async function writeSettings(settingsPath, settings) {
   await mkdir(dirname(settingsPath), { recursive: true });
   const tmpPath = `${settingsPath}.tmp`;
-  await writeFile(tmpPath, JSON.stringify(settings, null, 4), "utf8");
-  await rename(tmpPath, settingsPath);
+  await writeFile2(tmpPath, JSON.stringify(settings, null, 4), "utf8");
+  await rename2(tmpPath, settingsPath);
 }
 function checkHookPresence(groups, targetCmd) {
   let foundMigrate = false;
@@ -10086,8 +10148,8 @@ ${ONEBRAIN_MARKER}
 ${PATH_EXPORT}
 `;
   const tmpPath = `${profilePath}.tmp`;
-  await writeFile(tmpPath, updated, "utf8");
-  await rename(tmpPath, profilePath);
+  await writeFile2(tmpPath, updated, "utf8");
+  await rename2(tmpPath, profilePath);
 }
 async function runRegisterHooks(opts = {}) {
   const vaultRoot = opts.vaultDir ?? process.cwd();
@@ -10216,19 +10278,13 @@ __export(exports_vault_sync, {
   vaultSyncCommand: () => vaultSyncCommand,
   runVaultSync: () => runVaultSync
 });
-import {
-  mkdir as mkdir2,
-  mkdtemp,
-  readFile as readFile2,
-  readdir,
-  rename as rename2,
-  rm,
-  stat as stat3,
-  unlink,
-  writeFile as writeFile2
-} from "fs/promises";
+import { mkdir as mkdir2, mkdtemp, readFile as readFile2, readdir, rm, stat as stat3, unlink as unlink2, writeFile as writeFile3 } from "fs/promises";
 import { homedir as homedir2, tmpdir } from "os";
-import { dirname as dirname2, join as join5, relative } from "path";
+import { dirname as dirname2, join as join5, sep as pathSep, relative, resolve as resolvePath } from "path";
+function normalizePath(p2) {
+  const resolved = resolvePath(p2);
+  return resolved.endsWith(pathSep) && resolved.length > pathSep.length ? resolved.slice(0, -pathSep.length) : resolved;
+}
 function resolveBranch(updateChannel) {
   return updateChannel === "stable" ? "main" : "next";
 }
@@ -10250,7 +10306,7 @@ async function downloadTarball(branch, fetchFn) {
 }
 async function extractTarball(tarball, destDir) {
   const tarPath = join5(destDir, "bundle.tar.gz");
-  await writeFile2(tarPath, Buffer.from(tarball));
+  await writeFile3(tarPath, Buffer.from(tarball));
   const proc = Bun.spawn(["tar", "-xzf", tarPath, "-C", destDir], {
     stdout: "pipe",
     stderr: "pipe"
@@ -10260,7 +10316,7 @@ async function extractTarball(tarball, destDir) {
     const errText = await new Response(proc.stderr).text();
     throw new Error(`tar extraction failed (exit ${exitCode}): ${errText.trim()}`);
   }
-  await unlink(tarPath);
+  await unlink2(tarPath);
   const entries = await readdir(destDir);
   const topLevel = entries.find((e2) => e2 !== "bundle.tar.gz");
   if (!topLevel) {
@@ -10296,7 +10352,7 @@ async function listFilesRecursive(dir) {
   }
   return results;
 }
-async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink) {
+async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink2) {
   const sourcePlugin = join5(extractedDir, ".claude", "plugins", "onebrain");
   const destPlugin = join5(vaultRoot, ".claude", "plugins", "onebrain");
   await mkdir2(destPlugin, { recursive: true });
@@ -10316,7 +10372,7 @@ async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink) {
     const destPath = join5(destPlugin, rel);
     await mkdir2(dirname2(destPath), { recursive: true });
     const content = await readFile2(srcPath);
-    await writeFile2(destPath, content);
+    await writeFile3(destPath, content);
     filesAdded++;
   }
   let filesRemoved = 0;
@@ -10336,7 +10392,7 @@ async function copyRootDocs(extractedDir, vaultRoot) {
     const destPath = join5(vaultRoot, doc);
     try {
       const content = await readFile2(srcPath);
-      await writeFile2(destPath, content);
+      await writeFile3(destPath, content);
     } catch {}
   }
 }
@@ -10353,7 +10409,7 @@ async function mergeHarnessFile(extractedDir, vaultRoot, filename) {
   try {
     vaultText = await readFile2(destPath, "utf8");
   } catch {
-    await writeFile2(destPath, repoText, "utf8");
+    await writeFile3(destPath, repoText, "utf8");
     return repoText.split(`
 `).filter((l2) => l2.startsWith("@")).length;
   }
@@ -10374,7 +10430,7 @@ async function mergeHarnessFile(extractedDir, vaultRoot, filename) {
   }
   const merged = vaultLines.join(`
 `);
-  await writeFile2(destPath, merged, "utf8");
+  await writeFile3(destPath, merged, "utf8");
   return newImports.length;
 }
 async function mergeHarnessFiles(extractedDir, vaultRoot) {
@@ -10396,22 +10452,21 @@ async function updateVaultYml(vaultRoot, updateChannel) {
   }
   const raw = import_yaml3.parse(text) ?? {};
   raw["update_channel"] = updateChannel;
-  const updated = import_yaml3.stringify(raw, { lineWidth: 0 });
-  const tmpPath = `${vaultYmlPath}.tmp`;
-  await writeFile2(tmpPath, updated, "utf8");
-  await rename2(tmpPath, vaultYmlPath);
+  await atomicWrite(vaultYmlPath, import_yaml3.stringify(raw, { lineWidth: 0 }), "vault.yml");
 }
-async function readPluginVersion(vaultRoot) {
+async function readPluginMetadata(vaultRoot) {
   const pluginJsonPath = join5(vaultRoot, ".claude", "plugins", "onebrain", ".claude-plugin", "plugin.json");
   try {
     const text = await readFile2(pluginJsonPath, "utf8");
     const parsed = JSON.parse(text);
-    return typeof parsed["version"] === "string" ? parsed["version"] : "unknown";
+    const version = typeof parsed["version"] === "string" ? parsed["version"] : "unknown";
+    const lastUpdated = typeof parsed["lastUpdated"] === "string" ? parsed["lastUpdated"] : undefined;
+    return { version, lastUpdated };
   } catch {
-    return "unknown";
+    return { version: "unknown", lastUpdated: undefined };
   }
 }
-async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir) {
+async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir, now = () => new Date) {
   let text;
   try {
     text = await readFile2(installedPluginsPath, "utf8");
@@ -10433,8 +10488,12 @@ async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCache
     return { skipped: true };
   }
   const vaultPluginDir = join5(vaultRoot, ".claude", "plugins", "onebrain");
-  const pluginVersion = await readPluginVersion(vaultRoot);
+  const normalizedVaultRoot = normalizePath(vaultRoot);
+  const normalizedVaultPluginDir = normalizePath(vaultPluginDir);
+  const { version: pluginVersion, lastUpdated: pluginLastUpdated } = await readPluginMetadata(vaultRoot);
+  const updatedAt = pluginLastUpdated ?? now().toISOString();
   const cacheDir = installedPluginsCacheDir ?? join5(dirname2(installedPluginsPath), "cache");
+  const normalizedCacheDir = normalizePath(cacheDir);
   const hasMarketplace = onebrainKeys.some((k2) => {
     const entries = plugins[k2];
     return entries.some((e2) => e2["source"] === "marketplace");
@@ -10443,33 +10502,70 @@ async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCache
     return { skipped: true };
   }
   let changed = false;
+  const ONEBRAIN_KEY = "onebrain@onebrain";
+  if (Array.isArray(plugins[ONEBRAIN_KEY])) {
+    const before = plugins[ONEBRAIN_KEY];
+    const keep = [];
+    for (const entry of before) {
+      const projectPath = entry["projectPath"];
+      if (typeof projectPath !== "string") {
+        keep.push(entry);
+        continue;
+      }
+      try {
+        await stat3(projectPath);
+        keep.push(entry);
+      } catch (err) {
+        const code = err?.code;
+        if (code === "ENOENT")
+          continue;
+        process.stderr.write(`vault-sync: pin warning: stat ${projectPath}: ${code ?? "unknown"}
+`);
+        keep.push(entry);
+      }
+    }
+    if (keep.length !== before.length) {
+      plugins[ONEBRAIN_KEY] = keep;
+      changed = true;
+    }
+  }
   for (const key of onebrainKeys) {
     const entries = plugins[key];
     for (const entry of entries) {
-      const installPath = entry["installPath"];
-      if (typeof installPath !== "string") {
+      const installPathRaw = entry["installPath"];
+      const projectPathRaw = entry["projectPath"];
+      const installPathBad = installPathRaw !== undefined && typeof installPathRaw !== "string";
+      const projectPathBad = projectPathRaw !== undefined && typeof projectPathRaw !== "string";
+      if (installPathBad || projectPathBad) {
+        process.stderr.write(`vault-sync: pin warning: malformed entry \u2014 non-string installPath/projectPath in installed_plugins.json[${key}]
+`);
         continue;
       }
-      let inCache = false;
-      try {
-        inCache = installPath.startsWith(`${cacheDir}/`) || installPath === cacheDir;
-      } catch {
-        inCache = false;
-      }
-      if (!inCache) {
+      const installPath = typeof installPathRaw === "string" ? installPathRaw : undefined;
+      const projectPath = typeof projectPathRaw === "string" ? projectPathRaw : undefined;
+      const normalizedInstallPath = installPath !== undefined ? normalizePath(installPath) : undefined;
+      const normalizedProjectPath = projectPath !== undefined ? normalizePath(projectPath) : undefined;
+      const inCache = normalizedInstallPath !== undefined && (normalizedInstallPath === normalizedCacheDir || normalizedInstallPath.startsWith(`${normalizedCacheDir}${pathSep}`));
+      const isThisVault = normalizedInstallPath === normalizedVaultPluginDir;
+      const isThisProject = normalizedProjectPath === normalizedVaultRoot;
+      if (!isThisVault && !inCache && !isThisProject) {
         continue;
       }
-      entry["installPath"] = vaultPluginDir;
-      entry["version"] = pluginVersion;
-      changed = true;
+      if (normalizedInstallPath !== normalizedVaultPluginDir) {
+        entry["installPath"] = vaultPluginDir;
+        changed = true;
+      }
+      if (entry["version"] !== pluginVersion) {
+        entry["version"] = pluginVersion;
+        entry["lastUpdated"] = updatedAt;
+        changed = true;
+      }
     }
   }
   if (!changed) {
     return { skipped: false };
   }
-  const tmpPath = `${installedPluginsPath}.tmp`;
-  await writeFile2(tmpPath, JSON.stringify(data, null, 4), "utf8");
-  await rename2(tmpPath, installedPluginsPath);
+  await atomicWrite(installedPluginsPath, JSON.stringify(data, null, 4), "installed_plugins.json");
   return { skipped: false };
 }
 async function cleanPluginCache(installedPluginsPath, installedPluginsCacheDir) {
@@ -10535,7 +10631,7 @@ async function cleanPluginCache(installedPluginsPath, installedPluginsCacheDir)
 async function runVaultSync(vaultRoot, opts = {}) {
   const fetchFn = opts.fetchFn ?? globalThis.fetch;
   const isTTY = opts.isTTY ?? process.stdout.isTTY;
-  const unlinkFn = opts.unlinkFn ?? unlink;
+  const unlinkFn = opts.unlinkFn ?? unlink2;
   let updateChannel = "stable";
   try {
     const vaultYmlText = await readFile2(join5(vaultRoot, "vault.yml"), "utf8");
@@ -10637,7 +10733,7 @@ async function runVaultSync(vaultRoot, opts = {}) {
           const destPath = join5(destObsidian, rel);
           await mkdir2(dirname2(destPath), { recursive: true });
           const content = await readFile2(srcPath);
-          await writeFile2(destPath, content);
+          await writeFile3(destPath, content);
         }
       } catch {}
     }
@@ -10672,7 +10768,7 @@ async function runVaultSync(vaultRoot, opts = {}) {
     if (harness === "claude") {
       startSpinner("\uD83D\uDCCC", "Pinning to vault");
       try {
-        const pinResult = await pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir);
+        const pinResult = await pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir, opts.now);
         result.pinSkipped = pinResult.skipped;
         if (pinResult.skipped) {
           stopSpinner("pin skipped (not found or marketplace)");
@@ -10727,6 +10823,7 @@ async function vaultSyncCommand(vaultRoot, opts = {}) {
 var import_picocolors6, import_yaml3;
 var init_vault_sync = __esm(() => {
   init_dist2();
+  init_lib();
   init_cli_ui();
   init_harness();
   import_picocolors6 = __toESM(require_picocolors(), 1);
@@ -10761,7 +10858,7 @@ var import_picocolors5 = __toESM(require_picocolors(), 1);
 var import_picocolors = __toESM(require_picocolors(), 1);
 function resolveBinaryVersion() {
   if (true)
-    return "2.1.10";
+    return "2.1.12";
   try {
     const pkg = require_package();
     return pkg.version ?? "dev";
@@ -11229,6 +11326,7 @@ async function runDoctor(opts = {}) {
   const checkPluginFilesFn = opts.checkPluginFilesFn ?? checkPluginFiles;
   const checkVaultYmlKeysFn = opts.checkVaultYmlKeysFn ?? checkVaultYmlKeys;
   const checkSettingsHooksFn = opts.checkSettingsHooksFn ?? checkSettingsHooks;
+  const checkClaudeSettingsFn = opts.checkClaudeSettingsFn ?? checkClaudeSettings;
   if (isTTY) {
     await printBanner();
   }
@@ -11259,7 +11357,14 @@ async function runDoctor(opts = {}) {
   if (vaultYmlResult.status === "ok") {
     try {
       config = await loadVaultConfigFn(vaultDir);
-    } catch {}
+    } catch (err) {
+      const code = err?.code;
+      if (code !== "ENOENT") {
+        const msg = err instanceof Error ? err.message : String(err);
+        process.stderr.write(`doctor: vault.yml load warning: ${msg}
+`);
+      }
+    }
   }
   await randDelay();
   sp1?.stop(fmtResult(vaultYmlResult), vaultYmlResult.details);
@@ -11269,6 +11374,7 @@ async function runDoctor(opts = {}) {
   let pluginFilesResult;
   let vaultYmlKeysResult;
   let settingsHooksResult;
+  let claudeSettingsResult;
   if (isTTY) {
     const sp2 = createStep("\u2699\uFE0F", "Config schema");
     vaultYmlKeysResult = await checkVaultYmlKeysFn(vaultDir);
@@ -11294,6 +11400,10 @@ async function runDoctor(opts = {}) {
     qmdResult = await checkQmdEmbeddingsFn(config);
     await randDelay();
     sp7.stop(fmtResult(qmdResult), qmdResult.details);
+    const sp8 = createStep("\uD83D\uDED2", "Marketplace config");
+    claudeSettingsResult = await checkClaudeSettingsFn(vaultDir);
+    await randDelay();
+    sp8.stop(fmtResult(claudeSettingsResult), claudeSettingsResult.details);
   } else {
     [
       foldersResult,
@@ -11301,14 +11411,16 @@ async function runDoctor(opts = {}) {
       orphanResult,
       pluginFilesResult,
       vaultYmlKeysResult,
-      settingsHooksResult
+      settingsHooksResult,
+      claudeSettingsResult
     ] = await Promise.all([
       checkFoldersFn(vaultDir, config),
       checkQmdEmbeddingsFn(config),
       checkOrphanCheckpointsFn(vaultDir, config),
       checkPluginFilesFn(vaultDir),
       checkVaultYmlKeysFn(vaultDir),
-      checkSettingsHooksFn(vaultDir, config)
+      checkSettingsHooksFn(vaultDir, config),
+      checkClaudeSettingsFn(vaultDir)
     ]);
   }
   const results = [
@@ -11318,7 +11430,8 @@ async function runDoctor(opts = {}) {
     pluginFilesResult,
     settingsHooksResult,
     orphanResult,
-    qmdResult
+    qmdResult,
+    claudeSettingsResult
   ];
   const totalChecks = results.length;
   const errorCount = results.filter((r2) => r2.status === "error").length;
@@ -11351,14 +11464,17 @@ async function runDoctor(opts = {}) {
 `);
     }
   }
+  let fixFailedCount = 0;
   if (opts.fix) {
-    await applyFixes(vaultDir, results, isTTY, opts.registerHooksFn);
+    fixFailedCount = await applyFixes(vaultDir, results, isTTY, opts.registerHooksFn);
   }
+  const ok = errorCount === 0 && fixFailedCount === 0;
   return {
-    ok: errorCount === 0,
-    exitCode: errorCount > 0 ? 1 : 0,
+    ok,
+    exitCode: ok ? 0 : 1,
     errorCount,
-    warningCount
+    warningCount,
+    fixFailedCount
   };
 }
 async function doctorCommand(opts = {}) {
@@ -11406,12 +11522,18 @@ function getFix(r2) {
     };
   }
   const hasDeprecatedKeys = r2.details?.some((d) => d.includes("deprecated key: onebrain_version") || d.includes("deprecated key: method") || d.includes("deprecated key: runtime.harness"));
-  if (r2.check === "vault.yml-keys" && r2.status === "warn" && hasDeprecatedKeys) {
+  const hasMissingUpdateChannel = r2.details?.some((d) => d === "missing key: update_channel");
+  if (r2.check === "vault.yml-keys" && r2.status === "warn" && (hasDeprecatedKeys || hasMissingUpdateChannel)) {
     const deprecated = (r2.details ?? []).filter((d) => d.startsWith("deprecated key:")).map((d) => d.slice("deprecated key: ".length).split(" ")[0] ?? d);
-    const description = deprecated.length > 0 ? `Remove deprecated keys from vault.yml: ${deprecated.join(", ")}` : "Remove deprecated keys from vault.yml";
+    const fixParts = [];
+    if (hasMissingUpdateChannel)
+      fixParts.push("add update_channel: stable");
+    if (deprecated.length > 0)
+      fixParts.push(`remove deprecated: ${deprecated.join(", ")}`);
+    const description = fixParts.length > 0 ? `Fix vault.yml: ${fixParts.join("; ")}` : "Fix vault.yml";
     return {
       fn: async (vaultDir) => {
-        const { readFile: readFile2, writeFile: writeFile2, rename: rename2 } = await import("fs/promises");
+        const { readFile: readFile2 } = await import("fs/promises");
         const { join: join5 } = await import("path");
         const { parse: parse3, stringify } = await Promise.resolve().then(() => __toESM(require_dist(), 1));
         const vaultYmlPath = join5(vaultDir, "vault.yml");
@@ -11431,10 +11553,10 @@ function getFix(r2) {
             }
           }
         }
-        const updated = stringify(raw, { lineWidth: 0 });
-        const tmpPath = `${vaultYmlPath}.tmp`;
-        await writeFile2(tmpPath, updated, "utf8");
-        await rename2(tmpPath, vaultYmlPath);
+        if (details.some((d) => d === "missing key: update_channel")) {
+          raw["update_channel"] = "stable";
+        }
+        await atomicWrite(vaultYmlPath, stringify(raw, { lineWidth: 0 }), "vault.yml");
       },
       description
     };
@@ -11469,6 +11591,29 @@ function getFix(r2) {
       description: `Embed ${count} unembedded document(s) (qmd update + embed)`
     };
   }
+  if (r2.check === "claude-settings" && r2.status === "warn" && r2.details?.some((d) => d.startsWith("stale extraKnownMarketplaces.onebrain.source.repo:"))) {
+    return {
+      fn: async (vaultDir) => {
+        const { readFile: readFile2 } = await import("fs/promises");
+        const { join: join5 } = await import("path");
+        const settingsPath = join5(vaultDir, ".claude", "settings.json");
+        const text = await readFile2(settingsPath, "utf8");
+        const raw = JSON.parse(text);
+        const marketplaces = raw["extraKnownMarketplaces"];
+        const onebrain = marketplaces?.["onebrain"];
+        const source = onebrain?.["source"];
+        if (!source || source["repo"] !== "kengio/onebrain")
+          return;
+        source["repo"] = "onebrain-ai/onebrain";
+        const trailingNewline = text.endsWith(`
+`) ? `
+` : "";
+        const updated = `${JSON.stringify(raw, null, 2)}${trailingNewline}`;
+        await atomicWrite(settingsPath, updated, ".claude/settings.json");
+      },
+      description: "Rewrite stale marketplace repo: kengio/onebrain \u2192 onebrain-ai/onebrain"
+    };
+  }
   if (r2.check === "folders" && r2.status === "error" && r2.hint) {
     const missingStr = r2.hint.replace("Missing: ", "");
     return {
@@ -11492,7 +11637,7 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
       writeLine(`${import_picocolors5.default.green("\u25C6")}  Nothing to fix`);
     else
       writeLine("nothing to fix");
-    return;
+    return 0;
   }
   if (isTTY) {
     writeLine("");
@@ -11507,12 +11652,13 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
       barLine(import_picocolors5.default.dim("No"));
       barBlank();
       close(`No changes made \u2014 run ${import_picocolors5.default.cyan("onebrain doctor --fix")} to apply`);
-      return;
+      return 0;
     }
     barLine("Yes");
     barBlank();
   }
   let fixed = 0;
+  let fixFailed = 0;
   const unfixable = [];
   for (const r2 of results) {
     if (r2.status === "ok")
@@ -11528,6 +11674,7 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
       if (isTTY)
         barLine(`${import_picocolors5.default.green("\u25C6")}  ${fix.description}`);
     } catch (err) {
+      fixFailed++;
       const errMsg = err instanceof Error ? err.message : String(err);
       if (isTTY) {
         barLine(`${import_picocolors5.default.yellow("\u25B2")}  Could not fix ${r2.check}: ${errMsg}`);
@@ -11541,6 +11688,9 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
     barBlank();
     if (fixed > 0)
       barLine(`${import_picocolors5.default.green("\u25C6")}  Fixed ${fixed} issue(s)`);
+    if (fixFailed > 0) {
+      barLine(`${import_picocolors5.default.yellow("\u25B2")}  ${fixFailed} fix(es) failed \u2014 see warnings above`);
+    }
     if (unfixable.length > 0) {
       barLine(`${import_picocolors5.default.yellow("\u25B2")}  ${unfixable.length} issue(s) require manual action:`);
       for (const r2 of unfixable) {
@@ -11551,18 +11701,22 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
     close("Done");
   } else {
     process.stdout.write(`fixed: ${fixed}
+`);
+    if (fixFailed > 0)
+      process.stdout.write(`fix-failed: ${fixFailed}
 `);
     if (unfixable.length > 0) {
       process.stdout.write(`manual: ${unfixable.map((r2) => r2.check).join(", ")}
 `);
     }
   }
+  return fixFailed;
 }
 
 // src/commands/init.ts
 var import_picocolors7 = __toESM(require_picocolors(), 1);
 var import_yaml4 = __toESM(require_dist(), 1);
-import { mkdir as mkdir3, readFile as readFile3, readdir as readdir2, rename as rename3, stat as stat4, writeFile as writeFile3 } from "fs/promises";
+import { mkdir as mkdir3, readFile as readFile3, readdir as readdir2, rename as rename3, stat as stat4, writeFile as writeFile4 } from "fs/promises";
 import { homedir as homedir3 } from "os";
 import { dirname as dirname3, join as join6 } from "path";
 init_cli_ui();
@@ -11617,7 +11771,7 @@ var VAULT_YML_DEFAULTS = {
 };
 async function writeVaultYml(vaultDir) {
   const content = import_yaml4.stringify(VAULT_YML_DEFAULTS, { lineWidth: 0 });
-  await writeFile3(join6(vaultDir, "vault.yml"), content, "utf8");
+  await writeFile4(join6(vaultDir, "vault.yml"), content, "utf8");
 }
 async function downloadPluginFiles(vaultDir, vaultSyncFn) {
   const pluginJsonPath = join6(vaultDir, ".claude", "plugins", "onebrain", ".claude-plugin", "plugin.json");
@@ -11706,7 +11860,7 @@ async function registerPlugin(vaultDir, installedPluginsPath) {
   const tmpPath = `${installedPluginsPath}.tmp`;
   try {
     await mkdir3(dirname3(installedPluginsPath), { recursive: true });
-    await writeFile3(tmpPath, JSON.stringify(data, null, 4), "utf8");
+    await writeFile4(tmpPath, JSON.stringify(data, null, 4), "utf8");
     await rename3(tmpPath, installedPluginsPath);
   } catch (err) {
     const msg = err instanceof Error ? err.message : String(err);
@@ -11817,7 +11971,7 @@ async function installObsidianPlugins(vaultDir, opts) {
           throw new Error(`HTTP ${resp.status}`);
         }
         const buf = await resp.arrayBuffer();
-        await writeFile3(join6(pluginDir, assetName), Buffer.from(buf));
+        await writeFile4(join6(pluginDir, assetName), Buffer.from(buf));
       } catch (err) {
         if (assetName === "styles.css")
           continue;
@@ -12201,7 +12355,7 @@ async function checkpointCommand(mode, token, vaultRoot) {
 // src/commands/internal/migrate.ts
 init_lib();
 var import_yaml5 = __toESM(require_dist(), 1);
-import { readFile as readFile4, readdir as readdir3, writeFile as writeFile4 } from "fs/promises";
+import { readFile as readFile4, readdir as readdir3, writeFile as writeFile5 } from "fs/promises";
 import { join as join8 } from "path";
 function parseFrontmatterWithRest(rawText) {
   const text = rawText.replace(/\r\n/g, `
@@ -12285,7 +12439,7 @@ async function runBackfillRecapped(logsFolder, cutoffDate) {
           const updatedContent = `---
 ${updatedFm}---
 ${rest}`;
-          await writeFile4(fpath, updatedContent, "utf8");
+          await writeFile5(fpath, updatedContent, "utf8");
           backfilled++;
         } catch (error) {
           process.stderr.write(`migrate: error processing ${fname}: ${error}
@@ -12451,7 +12605,7 @@ init_register_hooks();
 
 // src/commands/internal/session-init.ts
 init_lib();
-import { unlink as unlink2 } from "fs/promises";
+import { unlink as unlink3 } from "fs/promises";
 import { tmpdir as osTmpdir2 } from "os";
 import { join as join10 } from "path";
 var DAY_NAMES = ["Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"];
@@ -12564,7 +12718,7 @@ async function cleanStaleStateFile(token, tmpDir) {
     const mtimeMs = mtime instanceof Date ? mtime.getTime() : Number(mtime) * 1000;
     if (mtimeMs < processStartMs) {
       try {
-        await unlink2(stateFile);
+        await unlink3(stateFile);
       } catch {}
     }
   } catch {}
@@ -12848,8 +13002,8 @@ function patchUtf8(stream) {
 }
 
 // src/index.ts
-var VERSION = "2.1.10";
-var RELEASE_DATE = "2026-05-05";
+var VERSION = "2.1.12";
+var RELEASE_DATE = "2026-05-06";
 patchUtf8(process.stdout);
 patchUtf8(process.stderr);
 var VERSION_STRING = `OneBrain v${VERSION} \u2014 released ${RELEASE_DATE}`;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@onebrain-ai/cli",
-  "version": "2.1.10",
+  "version": "2.1.12",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",