@onebrain-ai/cli 2.0.5 → 2.0.6

package/dist/onebrain

@@ -10218,6 +10218,10 @@ var init_register_hooks = __esm(() => {
   NPM_GLOBAL_BIN = join4(homedir2(), ".npm-global", "bin");
 });
 
+// src/index.ts
+import { existsSync } from "fs";
+import { dirname as dirname6, join as join13 } from "path";
+
 // ../../node_modules/commander/esm.mjs
 var import__ = __toESM(require_commander(), 1);
 var {
@@ -10743,7 +10747,7 @@ init_dist();
 import { mkdir as mkdir3, readFile as readFile3, rename as rename3, stat as stat3, writeFile as writeFile3 } from "node:fs/promises";
 import { homedir as homedir3 } from "node:os";
 import { dirname as dirname3, join as join5 } from "node:path";
-var binaryVersion = "2.0.5";
+var binaryVersion = "2.0.6";
 var STANDARD_FOLDERS = [
   "00-inbox",
   "01-projects",
@@ -11024,7 +11028,7 @@ async function initCommand(opts = {}) {
 // src/commands/update.ts
 init_dist3();
 init_dist();
-import { readFile as readFile4, rename as rename4, writeFile as writeFile4 } from "node:fs/promises";
+import { access, readFile as readFile4, rename as rename4, writeFile as writeFile4 } from "node:fs/promises";
 import { join as join6 } from "node:path";
 var GITHUB_RELEASES_URL = "https://api.github.com/repos/kengio/onebrain/releases/latest";
 function resolveBranch2(channel) {
@@ -11135,6 +11139,19 @@ async function runUpdate(opts = {}) {
   } else {
     writeLine("OneBrain Update");
   }
+  try {
+    await access(join6(vaultDir, "vault.yml"));
+  } catch {
+    const msg = `vault.yml not found in ${vaultDir}. Run 'onebrain update' from inside an OneBrain vault.`;
+    if (isTTY) {
+      v2.error(msg);
+    } else {
+      writeLine(`error: ${msg}`);
+    }
+    result.error = msg;
+    result.exitCode = 1;
+    return result;
+  }
   let latestVersion;
   try {
     latestVersion = await fetchLatestVersion(fetchFn);
@@ -11165,30 +11182,47 @@ async function runUpdate(opts = {}) {
   }
   let filesAdded = 0;
   let filesRemoved = 0;
+  const syncSpinner = isTTY ? L2() : null;
+  syncSpinner?.start("Syncing plugin files…");
   try {
     const syncResult = await vaultSyncFn(vaultDir, { branch });
     filesAdded = syncResult.filesAdded;
     filesRemoved = syncResult.filesRemoved;
+    syncSpinner?.stop(`Synced — ${filesAdded} added, ${filesRemoved} removed`);
+    if (!isTTY) {
+      writeLine(`syncing: ${filesAdded} files synced, ${filesRemoved} removed`);
+    }
   } catch (err) {
     const msg = err instanceof Error ? err.message : String(err);
+    syncSpinner?.stop("Sync failed");
     result.error = `vault-sync failed: ${msg}`;
     result.exitCode = 1;
     process.stderr.write(`update: ${result.error}
 `);
     return result;
   }
-  noteStep("syncing", `${filesAdded} files synced, ${filesRemoved} removed`);
-  try {
-    await installBinaryFn(latestVersion);
-  } catch (err) {
-    const msg = err instanceof Error ? err.message : String(err);
-    result.error = `Binary install failed: ${msg}`;
-    result.exitCode = 1;
-    process.stderr.write(`update: ${result.error}
+  const needsBinaryUpdate = latestVersion !== currentVersion;
+  if (needsBinaryUpdate) {
+    const installSpinner = isTTY ? L2() : null;
+    installSpinner?.start(`Installing @onebrain-ai/cli ${latestVersion}…`);
+    try {
+      await installBinaryFn(latestVersion);
+      installSpinner?.stop(`Installed @onebrain-ai/cli ${latestVersion}`);
+      if (!isTTY) {
+        writeLine(`upgrading: @onebrain-ai/cli ${latestVersion} installed`);
+      }
+    } catch (err) {
+      const msg = err instanceof Error ? err.message : String(err);
+      installSpinner?.stop("Install failed");
+      result.error = `Binary install failed: ${msg}`;
+      result.exitCode = 1;
+      process.stderr.write(`update: ${result.error}
 `);
-    return result;
+      return result;
+    }
+  } else {
+    noteStep("binary", `@onebrain-ai/cli ${latestVersion} already up to date`);
   }
-  noteStep("upgrading", `@onebrain-ai/cli ${latestVersion} installed`);
   const binaryValid = await validateBinaryFn();
   if (!binaryValid) {
     result.error = "Binary validation failed. Check PATH. register-hooks NOT called.";
@@ -11245,7 +11279,6 @@ async function updateCommand(opts = {}) {
 
 // src/internal/checkpoint.ts
 import { readFileSync, readdirSync, writeFileSync } from "node:fs";
-import { mkdir as mkdir4, readdir as readdir2, writeFile as writeFile5 } from "node:fs/promises";
 import { tmpdir as osTmpdir } from "node:os";
 import { join as join7 } from "node:path";
 var SKIP_WINDOW = 60;
@@ -11267,15 +11300,13 @@ function readState(token, tmpDir = osTmpdir()) {
     const count = Number(parts[0]);
     const last_ts = Number(parts[1]);
     const last_stop_nn = parts[2] ?? "00";
-    const pending_stub = parts[3] && parts[3].length > 0 ? parts[3] : undefined;
     if (!Number.isInteger(count) || !Number.isInteger(last_ts) || !/^\d{2}$/.test(last_stop_nn)) {
       throw new Error("malformed state");
     }
-    return { count, last_ts, last_stop_nn, pending_stub };
+    return { count, last_ts, last_stop_nn };
   } catch {
-    const now = Math.floor(Date.now() / 1000);
     try {
-      writeFileSync(stateFilePath(token, tmpDir), `0:${now}:00`, "utf8");
+      writeFileSync(stateFilePath(token, tmpDir), "0:0:00", "utf8");
     } catch (writeErr) {
       process.stderr.write(`checkpoint: failed to rewrite state file for token ${token}: ${writeErr}
 `);
@@ -11289,8 +11320,7 @@ function readState(token, tmpDir = osTmpdir()) {
 }
 function writeState(token, state, tmpDir = osTmpdir()) {
   const path = stateFilePath(token, tmpDir);
-  const base = `${state.count}:${state.last_ts}:${state.last_stop_nn}`;
-  const content = state.pending_stub !== undefined ? `${base}:${state.pending_stub}` : base;
+  const content = `${state.count}:${state.last_ts}:${state.last_stop_nn}`;
   try {
     writeFileSync(path, content, "utf8");
   } catch (err) {
@@ -11357,12 +11387,6 @@ function formatDate(epochSeconds) {
   const dd = String(d2.getDate()).padStart(2, "0");
   return `${yyyy}-${mm}-${dd}`;
 }
-function formatYYYY(epochSeconds) {
-  return new Date(epochSeconds * 1000).getFullYear().toString();
-}
-function formatMM(epochSeconds) {
-  return String(new Date(epochSeconds * 1000).getMonth() + 1).padStart(2, "0");
-}
 function emitBlock(reason) {
   process.stdout.write(`${JSON.stringify({ decision: "block", reason })}
 `);
@@ -11394,156 +11418,26 @@ function handleStop(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDi
   const since = maxNn === 0 ? " since start" : ` since checkpoint-${String(maxNn).padStart(2, "0")}`;
   const filename = `${date}-${token}-checkpoint-${nextNn}.md`;
   emitBlock(`${filename}${since}`);
-  writeState(token, { count: 0, last_ts: now, last_stop_nn: nextNn, pending_stub: state.pending_stub }, tmpDir);
+  writeState(token, { count: 0, last_ts: now, last_stop_nn: nextNn }, tmpDir);
 }
-var PRECOMPACT_STUB_TEMPLATE = (date, nn) => `---
-tags: [checkpoint, session-log]
-date: ${date}
-checkpoint: ${nn}
-trigger: precompact
-merged: false
----
-
-## What We Worked On
-
-<!-- stub: written automatically before compact — fill in via postcompact -->
-
-## Key Decisions
-
--
-
-## Insights & Learnings
-
--
-
-## What Worked / Didn't Work
-
--
-
-## Action Items
-
--
-
-## Open Questions
-
--
-`;
-async function handlePrecompact(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
+function handlePrecompact(token, _vaultRoot, now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
   const state = readState(token, tmpDir);
   if (state.last_ts > 0 && now - state.last_ts < PRECOMPACT_RECENCY) {
     return;
   }
-  if (state.pending_stub) {
-    return;
-  }
-  const date = formatDate(now);
-  let logsFolder = DEFAULT_LOGS_FOLDER;
-  try {
-    const config = await loadVaultConfig(vaultRoot);
-    logsFolder = config.folders.logs;
-  } catch {}
-  const yyyy = formatYYYY(now);
-  const mm = formatMM(now);
-  const stubDir = join7(vaultRoot, logsFolder, yyyy, mm);
-  const existingFiles = await readdir2(stubDir).catch(() => []);
-  const prefix = `${date}-${token}-checkpoint-`;
-  const maxNn = existingFiles.reduce((max, f2) => {
-    if (!f2.startsWith(prefix) || !f2.endsWith(".md"))
-      return max;
-    const m3 = f2.match(/-checkpoint-(\d{2})\.md$/);
-    return m3 ? Math.max(max, Number(m3[1])) : max;
-  }, 0);
-  const stubNn = String(maxNn + 1).padStart(2, "0");
-  const stubFilename = `${date}-${token}-checkpoint-${stubNn}.md`;
-  const stubPath = join7(stubDir, stubFilename);
-  try {
-    await mkdir4(stubDir, { recursive: true });
-    await writeFile5(stubPath, PRECOMPACT_STUB_TEMPLATE(date, stubNn), "utf8");
-  } catch (err) {
-    process.stderr.write(`checkpoint: failed to write stub file ${stubPath}: ${err}
-`);
-    return;
-  }
-  writeState(token, {
-    count: 0,
-    last_ts: state.last_ts,
-    last_stop_nn: state.last_stop_nn,
-    pending_stub: stubFilename
-  }, tmpDir);
+  writeState(token, { count: 0, last_ts: state.last_ts, last_stop_nn: state.last_stop_nn }, tmpDir);
 }
-function handlePostcompact(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
+function handlePostcompact(token, _vaultRoot, now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
   const state = readState(token, tmpDir);
-  if (!state.pending_stub) {
+  if (state.last_ts > 0 && now - state.last_ts < PRECOMPACT_RECENCY) {
     writeState(token, { count: 0, last_ts: state.last_ts, last_stop_nn: state.last_stop_nn }, tmpDir);
     return;
   }
-  const stubNnMatch = state.pending_stub.match(/-checkpoint-(\d{2})\.md$/);
-  const stubNn = stubNnMatch?.[1] ?? "01";
-  const stubNnNum = Number(stubNn);
-  const { logsFolder } = loadVaultSettings(vaultRoot);
-  const date = state.pending_stub.slice(0, 10);
-  const yyyy = date.slice(0, 4);
-  const mm = date.slice(5, 7);
-  const dir = join7(vaultRoot, logsFolder, yyyy, mm);
-  const prefix = `${date}-${token}-checkpoint-`;
-  let predecessorNn = 0;
-  try {
-    for (const f2 of readdirSync(dir)) {
-      if (!f2.startsWith(prefix) || !f2.endsWith(".md"))
-        continue;
-      const m3 = f2.match(/-checkpoint-(\d{2})\.md$/);
-      if (m3) {
-        const nn = Number(m3[1]);
-        if (nn < stubNnNum)
-          predecessorNn = Math.max(predecessorNn, nn);
-      }
-    }
-  } catch {}
-  const since = predecessorNn === 0 ? " since start" : ` since checkpoint-${String(predecessorNn).padStart(2, "0")}`;
-  emitBlock(`fill-checkpoint: ${state.pending_stub}${since}`);
-  writeState(token, { count: 0, last_ts: now, last_stop_nn: stubNn }, tmpDir);
+  emitBlock(`auto-wrapup: ${token}`);
+  writeState(token, { count: 0, last_ts: now, last_stop_nn: state.last_stop_nn }, tmpDir);
 }
 function postcompactFallback(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
-  const state = readState(token, tmpDir);
-  if (state.pending_stub) {
-    handlePostcompact(token, vaultRoot, now, tmpDir);
-    return;
-  }
-  const { logsFolder } = loadVaultSettings(vaultRoot);
-  const date = formatDate(now);
-  const yyyy = date.slice(0, 4);
-  const mm = date.slice(5, 7);
-  const dir = join7(vaultRoot, logsFolder, yyyy, mm);
-  const prefix = `${date}-${token}-checkpoint-`;
-  const stubs = [];
-  const allNns = [];
-  try {
-    for (const f2 of readdirSync(dir)) {
-      if (!f2.startsWith(prefix) || !f2.endsWith(".md"))
-        continue;
-      const m3 = f2.match(/-checkpoint-(\d{2})\.md$/);
-      if (!m3)
-        continue;
-      allNns.push(Number(m3[1]));
-      const content = readFileSync(join7(dir, f2), "utf8");
-      if (/^trigger:\s*precompact/m.test(content) && !/^merged:\s*true/m.test(content)) {
-        stubs.push(f2);
-      }
-    }
-  } catch {}
-  if (stubs.length === 0) {
-    writeState(token, { count: 0, last_ts: state.last_ts, last_stop_nn: state.last_stop_nn }, tmpDir);
-    return;
-  }
-  stubs.sort();
-  const stubFilename = stubs[stubs.length - 1];
-  const stubNnMatch = stubFilename.match(/-checkpoint-(\d{2})\.md$/);
-  const stubNn = stubNnMatch?.[1] ?? "01";
-  const stubNnNum = Number(stubNn);
-  const predecessorNn = allNns.filter((n) => n < stubNnNum).reduce((max, n) => Math.max(max, n), 0);
-  const since = predecessorNn === 0 ? " since start" : ` since checkpoint-${String(predecessorNn).padStart(2, "0")}`;
-  emitBlock(`fill-checkpoint: ${stubFilename}${since}`);
-  writeState(token, { count: 0, last_ts: now, last_stop_nn: stubNn }, tmpDir);
+  handlePostcompact(token, vaultRoot, now, tmpDir);
 }
 async function checkpointCommand(mode, token, vaultRoot) {
   try {
@@ -11552,7 +11446,7 @@ async function checkpointCommand(mode, token, vaultRoot) {
         handleStop(token, vaultRoot);
         break;
       case "precompact":
-        await handlePrecompact(token, vaultRoot);
+        handlePrecompact(token, vaultRoot);
         break;
       case "postcompact":
         postcompactFallback(token, vaultRoot);
@@ -11571,7 +11465,7 @@ async function checkpointCommand(mode, token, vaultRoot) {
 }
 
 // src/internal/migrate.ts
-import { readFile as readFile5, readdir as readdir3, writeFile as writeFile6 } from "node:fs/promises";
+import { readFile as readFile5, readdir as readdir2, writeFile as writeFile5 } from "node:fs/promises";
 import { join as join8 } from "node:path";
 init_dist();
 function parseFrontmatterWithRest(rawText) {
@@ -11600,7 +11494,7 @@ function parseFrontmatterWithRest(rawText) {
 }
 async function listMdFiles(dir) {
   try {
-    const entries = await readdir3(dir);
+    const entries = await readdir2(dir);
     return entries.filter((e2) => e2.endsWith(".md"));
   } catch {
     return [];
@@ -11612,7 +11506,7 @@ async function runBackfillRecapped(logsFolder) {
   let skipped = 0;
   let yearDirs = [];
   try {
-    yearDirs = await readdir3(logsFolder);
+    yearDirs = await readdir2(logsFolder);
   } catch {
     return { backfilled: 0, skipped: 0 };
   }
@@ -11620,7 +11514,7 @@ async function runBackfillRecapped(logsFolder) {
     const yearPath = join8(logsFolder, yearDir);
     let monthDirs = [];
     try {
-      monthDirs = await readdir3(yearPath);
+      monthDirs = await readdir2(yearPath);
     } catch {
       continue;
     }
@@ -11650,7 +11544,7 @@ async function runBackfillRecapped(logsFolder) {
           const updatedContent = `---
 ${updatedFm}---
 ${rest}`;
-          await writeFile6(fpath, updatedContent, "utf8");
+          await writeFile5(fpath, updatedContent, "utf8");
           backfilled++;
         } catch (error) {
           process.stderr.write(`migrate: error processing ${fname}: ${error}
@@ -11683,7 +11577,7 @@ async function migrateCommand(migrationName) {
 
 // src/internal/orphan-scan.ts
 init_dist();
-import { readFile as readFile6, readdir as readdir4 } from "node:fs/promises";
+import { readFile as readFile6, readdir as readdir3 } from "node:fs/promises";
 import { join as join9 } from "node:path";
 function parseFrontmatter(rawText) {
   const text = rawText.replace(/\r\n/g, `
@@ -11712,7 +11606,7 @@ function getMonthParts(now = new Date) {
 }
 async function listMdFiles2(dir) {
   try {
-    const entries = await readdir4(dir);
+    const entries = await readdir3(dir);
     return entries.filter((e2) => e2.endsWith(".md"));
   } catch {
     return [];
@@ -11820,7 +11714,7 @@ async function qmdReindexCommand(vaultRoot) {
 // src/internal/register-hooks.ts
 init_dist3();
 init_dist();
-import { mkdir as mkdir5, readFile as readFile7, rename as rename5, writeFile as writeFile7 } from "node:fs/promises";
+import { mkdir as mkdir4, readFile as readFile7, rename as rename5, writeFile as writeFile6 } from "node:fs/promises";
 import { homedir as homedir4 } from "node:os";
 import { dirname as dirname4, join as join10 } from "node:path";
 var HOOK_COMMANDS2 = {
@@ -11850,9 +11744,9 @@ async function readSettings2(settingsPath) {
   }
 }
 async function writeSettings2(settingsPath, settings) {
-  await mkdir5(dirname4(settingsPath), { recursive: true });
+  await mkdir4(dirname4(settingsPath), { recursive: true });
   const tmpPath = `${settingsPath}.tmp`;
-  await writeFile7(tmpPath, JSON.stringify(settings, null, 4), "utf8");
+  await writeFile6(tmpPath, JSON.stringify(settings, null, 4), "utf8");
   await rename5(tmpPath, settingsPath);
 }
 function checkHookPresence2(groups, targetCmd) {
@@ -11981,7 +11875,7 @@ ${ONEBRAIN_MARKER2}
 ${PATH_EXPORT2}
 `;
   const tmpPath = `${profilePath}.tmp`;
-  await writeFile7(tmpPath, updated, "utf8");
+  await writeFile6(tmpPath, updated, "utf8");
   await rename5(tmpPath, profilePath);
 }
 async function runRegisterHooks2(opts = {}) {
@@ -12240,15 +12134,15 @@ async function sessionInitCommand(vaultRoot) {
 init_dist3();
 init_dist();
 import {
-  mkdir as mkdir6,
+  mkdir as mkdir5,
   mkdtemp as mkdtemp2,
   readFile as readFile8,
-  readdir as readdir5,
+  readdir as readdir4,
   rename as rename6,
   rm as rm2,
   stat as stat4,
   unlink as unlink3,
-  writeFile as writeFile8
+  writeFile as writeFile7
 } from "node:fs/promises";
 import { homedir as homedir5, tmpdir as tmpdir2 } from "node:os";
 import { dirname as dirname5, join as join12, relative as relative2 } from "node:path";
@@ -12273,7 +12167,7 @@ async function downloadTarball2(branch, fetchFn) {
 }
 async function extractTarball2(tarball, destDir) {
   const tarPath = join12(destDir, "bundle.tar.gz");
-  await writeFile8(tarPath, Buffer.from(tarball));
+  await writeFile7(tarPath, Buffer.from(tarball));
   const proc = Bun.spawn(["tar", "-xzf", tarPath, "-C", destDir], {
     stdout: "pipe",
     stderr: "pipe"
@@ -12284,7 +12178,7 @@ async function extractTarball2(tarball, destDir) {
     throw new Error(`tar extraction failed (exit ${exitCode}): ${errText.trim()}`);
   }
   await unlink3(tarPath);
-  const entries = await readdir5(destDir);
+  const entries = await readdir4(destDir);
   const topLevel = entries.find((e2) => e2 !== "bundle.tar.gz");
   if (!topLevel) {
     throw new Error("Extracted tarball contains no top-level directory");
@@ -12298,7 +12192,7 @@ async function listFilesRecursive2(dir) {
     const current = queue.pop();
     let entries;
     try {
-      entries = await readdir5(current);
+      entries = await readdir4(current);
     } catch {
       continue;
     }
@@ -12322,7 +12216,7 @@ async function listFilesRecursive2(dir) {
 async function syncPluginFiles2(extractedDir, vaultRoot, unlinkFn = unlink3) {
   const sourcePlugin = join12(extractedDir, ".claude", "plugins", "onebrain");
   const destPlugin = join12(vaultRoot, ".claude", "plugins", "onebrain");
-  await mkdir6(destPlugin, { recursive: true });
+  await mkdir5(destPlugin, { recursive: true });
   const sourceFiles = await listFilesRecursive2(sourcePlugin);
   const sourceRelSet = new Set(sourceFiles.map((f2) => relative2(sourcePlugin, f2)));
   const destFiles = await listFilesRecursive2(destPlugin);
@@ -12337,9 +12231,9 @@ async function syncPluginFiles2(extractedDir, vaultRoot, unlinkFn = unlink3) {
   for (const srcPath of sourceFiles) {
     const rel = relative2(sourcePlugin, srcPath);
     const destPath = join12(destPlugin, rel);
-    await mkdir6(dirname5(destPath), { recursive: true });
+    await mkdir5(dirname5(destPath), { recursive: true });
     const content = await readFile8(srcPath);
-    await writeFile8(destPath, content);
+    await writeFile7(destPath, content);
     filesAdded++;
   }
   let filesRemoved = 0;
@@ -12359,7 +12253,7 @@ async function copyRootDocs2(extractedDir, vaultRoot) {
     const destPath = join12(vaultRoot, doc);
     try {
       const content = await readFile8(srcPath);
-      await writeFile8(destPath, content);
+      await writeFile7(destPath, content);
     } catch {}
   }
 }
@@ -12376,7 +12270,7 @@ async function mergeHarnessFile2(extractedDir, vaultRoot, filename) {
   try {
     vaultText = await readFile8(destPath, "utf8");
   } catch {
-    await writeFile8(destPath, repoText, "utf8");
+    await writeFile7(destPath, repoText, "utf8");
     return repoText.split(`
 `).filter((l2) => l2.startsWith("@")).length;
   }
@@ -12397,7 +12291,7 @@ async function mergeHarnessFile2(extractedDir, vaultRoot, filename) {
   }
   const merged = vaultLines.join(`
 `);
-  await writeFile8(destPath, merged, "utf8");
+  await writeFile7(destPath, merged, "utf8");
   return newImports.length;
 }
 async function mergeHarnessFiles2(extractedDir, vaultRoot) {
@@ -12422,7 +12316,7 @@ async function updateVaultYml2(vaultRoot, version, updateChannel) {
   raw.update_channel = updateChannel;
   const updated = $stringify(raw, { lineWidth: 0 });
   const tmpPath = `${vaultYmlPath}.tmp`;
-  await writeFile8(tmpPath, updated, "utf8");
+  await writeFile7(tmpPath, updated, "utf8");
   await rename6(tmpPath, vaultYmlPath);
 }
 async function readPluginVersion2(vaultRoot) {
@@ -12492,7 +12386,7 @@ async function pinToVault2(vaultRoot, installedPluginsPath, installedPluginsCach
     return { skipped: false };
   }
   const tmpPath = `${installedPluginsPath}.tmp`;
-  await writeFile8(tmpPath, JSON.stringify(data, null, 4), "utf8");
+  await writeFile7(tmpPath, JSON.stringify(data, null, 4), "utf8");
   await rename6(tmpPath, installedPluginsPath);
   return { skipped: false };
 }
@@ -12523,7 +12417,7 @@ async function cleanPluginCache2(installedPluginsPath, installedPluginsCacheDir)
   } catch {}
   if (onebrainDirs.length === 0) {
     try {
-      const marketplaceDirs = await readdir5(cacheDir);
+      const marketplaceDirs = await readdir4(cacheDir);
       for (const mp of marketplaceDirs) {
         const candidate = join12(cacheDir, mp, "onebrain");
         try {
@@ -12539,7 +12433,7 @@ async function cleanPluginCache2(installedPluginsPath, installedPluginsCacheDir)
   for (const pluginDir of onebrainDirs) {
     let versionDirs;
     try {
-      versionDirs = await readdir5(pluginDir);
+      versionDirs = await readdir4(pluginDir);
     } catch {
       continue;
     }
@@ -12726,7 +12620,7 @@ async function vaultSyncCommand2(vaultRoot, opts = {}) {
 }
 
 // src/index.ts
-var VERSION = "2.0.5";
+var VERSION = "2.0.6";
 var RELEASE_DATE = "2026-04-26";
 if (process.platform === "win32") {
   process.stdout.setDefaultEncoding("utf8");
@@ -12738,6 +12632,19 @@ if (process.argv.slice(2).length === 0) {
   console.log("Run `onebrain help` for available commands.");
   process.exit(0);
 }
+function findVaultRoot(startDir) {
+  if (!startDir)
+    return process.cwd();
+  let dir = startDir;
+  while (true) {
+    if (existsSync(join13(dir, "vault.yml")))
+      return dir;
+    const parent = dirname6(dir);
+    if (parent === dir)
+      return startDir;
+    dir = parent;
+  }
+}
 var program2 = new Command;
 program2.name("onebrain").description("OneBrain CLI \u2014 personal AI OS for Obsidian").version(VERSION_STRING, "-v, --version");
 program2.command("init").description("Initialize a new OneBrain vault").option("--vault-dir <path>", "vault root directory (default: cwd)").option("--harness <harness>", "harness type: claude-code | gemini | direct").option("--force", "overwrite existing vault.yml without prompting").action(async (opts) => {
@@ -12747,29 +12654,31 @@ program2.command("init").description("Initialize a new OneBrain vault").option("
     force: opts.force
   });
 });
-program2.command("update").description("Update OneBrain plugin files from GitHub").option("--check", "show what would change and exit without making changes").option("--channel <channel>", "update channel: stable | next").action(async (opts) => {
+program2.command("update").description("Update OneBrain plugin files from GitHub").option("--check", "show what would change and exit without making changes").option("--channel <channel>", "update channel: stable | next").option("--vault-dir <path>", "vault root directory (default: auto-detect from cwd)").action(async (opts) => {
   await updateCommand({
+    vaultDir: opts.vaultDir ?? findVaultRoot(process.cwd()),
     check: opts.check,
     channel: opts.channel
   });
 });
 program2.command("doctor").description("Run vault health checks and report issues").action(async () => {
-  const vaultRoot = process.cwd();
+  const vaultRoot = findVaultRoot(process.cwd());
   await doctorCommand({ vaultDir: vaultRoot, binaryVersion: VERSION });
 });
 program2.command("help").description("Show this help message").action(() => {
   program2.help();
 });
-program2.command("session-init", { hidden: true }).description("Emit session token and datetime (called by Claude Code hook)").action(async () => {
-  const vaultRoot = process.cwd();
+program2.command("session-init", { hidden: true }).description("Emit session token and datetime (called by Claude Code hook)").option("--vault-dir <path>", "vault root directory (default: auto-detect from cwd)").action(async (opts) => {
+  const vaultRoot = opts.vaultDir ?? findVaultRoot(process.cwd());
   await sessionInitCommand(vaultRoot);
 });
 program2.command("orphan-scan", { hidden: true }).description("Scan for orphaned checkpoint files in logs folder").argument("<logs_folder>", "path to logs folder").argument("<session_token>", "current session token to exclude").action(async (logsFolder, sessionToken) => {
   await orphanScanCommand(logsFolder, sessionToken);
 });
-program2.command("checkpoint", { hidden: true }).description("Handle checkpoint lifecycle (stop/precompact/postcompact/reset)").argument("<mode>", "stop | precompact | postcompact | reset").action(async (mode) => {
+program2.command("checkpoint", { hidden: true }).description("Handle checkpoint lifecycle (stop/precompact/postcompact/reset)").argument("<mode>", "stop | precompact | postcompact | reset").option("--vault-dir <path>", "vault root directory (default: auto-detect from cwd)").action(async (mode, opts) => {
   const token = await resolveSessionToken();
-  await checkpointCommand(mode, token, process.cwd());
+  const vaultRoot = opts.vaultDir ?? findVaultRoot(process.cwd());
+  await checkpointCommand(mode, token, vaultRoot);
 });
 program2.command("qmd-reindex", { hidden: true }).description("Trigger qmd index rebuild").action(async () => {
   const vaultRoot = process.cwd();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@onebrain-ai/cli",
-  "version": "2.0.5",
+  "version": "2.0.6",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",