@onebrain-ai/cli 2.0.2 → 2.0.4

package/README.md

@@ -0,0 +1,48 @@
+# @onebrain-ai/cli
+
+The CLI binary for [OneBrain](https://github.com/kengio/onebrain) — a personal AI OS built on Obsidian with persistent memory, 24+ skills, and Claude Code integration.
+
+## Install
+
+```bash
+# with bun (recommended)
+bun install -g @onebrain-ai/cli
+
+# or with npm
+npm install -g @onebrain-ai/cli
+```
+
+Verify: `onebrain --version`
+
+## What it does
+
+The `onebrain` binary handles the low-level operations that keep your vault running.
+
+**User-facing commands:**
+
+| Command | Purpose |
+|---------|---------|
+| `onebrain init` | First-time vault initialization |
+| `onebrain update` | Pull latest plugin files from GitHub |
+| `onebrain doctor` | Audit vault health — orphan checkpoints, version drift, qmd embedding status, missing config |
+| `onebrain help` | List all available commands |
+
+**Internal commands** (not meant to be run directly):
+
+`session-init` · `orphan-scan` · `checkpoint` · `qmd-reindex` · `vault-sync` · `register-hooks` · `migrate`
+
+## Requirements
+
+- macOS, Linux, or Windows (Git Bash)
+- Bun or Node.js required (used as the runtime for the npm package)
+- For a self-contained binary with no runtime dependency, download from [GitHub Releases](https://github.com/kengio/onebrain/releases)
+
+## OneBrain
+
+OneBrain gives your AI agent persistent memory across sessions, a structured Markdown vault, and 24+ pre-built skills — so every session picks up exactly where the last one left off.
+
+**Full documentation and vault setup:** [github.com/kengio/onebrain](https://github.com/kengio/onebrain)
+
+## License
+
+[MIT](https://github.com/kengio/onebrain/blob/main/LICENSE)

package/dist/onebrain

@@ -10742,7 +10742,7 @@ 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 = "2.0.2";
+var binaryVersion = "2.0.4";
 var STANDARD_FOLDERS = [
   "00-inbox",
   "01-projects",
@@ -11228,8 +11228,8 @@ async function updateCommand(opts = {}) {
 }
 
 // src/internal/checkpoint.ts
-import { readFileSync, writeFileSync } from "node:fs";
-import { mkdir as mkdir4, writeFile as writeFile5 } from "node:fs/promises";
+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;
@@ -11282,13 +11282,15 @@ function writeState(token, state, tmpDir = osTmpdir()) {
 `);
   }
 }
-function loadThresholds(vaultRoot) {
+var DEFAULT_LOGS_FOLDER = "07-logs";
+function loadVaultSettings(vaultRoot) {
   try {
     const vaultYml = join7(vaultRoot, "vault.yml");
     const raw = readFileSync(vaultYml, "utf8");
-    const checkpointBlock = raw.match(/^checkpoint:\s*\n((?:[ \t]+[^\n]+\n?)*)/m);
     let messages = DEFAULT_MESSAGES_THRESHOLD;
     let minutes = DEFAULT_MINUTES_THRESHOLD;
+    let logsFolder = DEFAULT_LOGS_FOLDER;
+    const checkpointBlock = raw.match(/^checkpoint:\s*\n((?:[ \t]+[^\n]+\n?)*)/m);
     if (checkpointBlock?.[1]) {
       const block = checkpointBlock[1];
       const msgMatch = block.match(/messages:\s*(\d+)/);
@@ -11298,14 +11300,40 @@ function loadThresholds(vaultRoot) {
       if (minMatch?.[1])
         minutes = Number(minMatch[1]);
     }
-    return { messagesThreshold: messages, minutesThreshold: minutes };
+    const foldersBlock = raw.match(/^folders:\s*\n((?:[ \t]+[^\n]+\n?)*)/m);
+    if (foldersBlock?.[1]) {
+      const logsMatch = foldersBlock[1].match(/logs:\s*['"]?([^'"\s]+)['"]?/);
+      if (logsMatch?.[1])
+        logsFolder = logsMatch[1];
+    }
+    return { messagesThreshold: messages, minutesThreshold: minutes, logsFolder };
   } catch {
     return {
       messagesThreshold: DEFAULT_MESSAGES_THRESHOLD,
-      minutesThreshold: DEFAULT_MINUTES_THRESHOLD
+      minutesThreshold: DEFAULT_MINUTES_THRESHOLD,
+      logsFolder: DEFAULT_LOGS_FOLDER
     };
   }
 }
+function maxCheckpointNnSync(vaultRoot, date, token, logsFolder) {
+  const yyyy = date.slice(0, 4);
+  const mm = date.slice(5, 7);
+  const dir = join7(vaultRoot, logsFolder, yyyy, mm);
+  const prefix = `${date}-${token}-checkpoint-`;
+  try {
+    let max = 0;
+    for (const f2 of readdirSync(dir)) {
+      if (!f2.startsWith(prefix) || !f2.endsWith(".md"))
+        continue;
+      const m3 = f2.match(/-checkpoint-(\d{2})\.md$/);
+      if (m3)
+        max = Math.max(max, Number(m3[1]));
+    }
+    return max;
+  } catch {
+    return 0;
+  }
+}
 function formatDate(epochSeconds) {
   const d2 = new Date(epochSeconds * 1000);
   const yyyy = d2.getFullYear().toString();
@@ -11332,7 +11360,7 @@ function handleStop(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDi
     return;
   }
   state.count += 1;
-  const { messagesThreshold, minutesThreshold } = loadThresholds(vaultRoot);
+  const { messagesThreshold, minutesThreshold, logsFolder } = loadVaultSettings(vaultRoot);
   const timeThreshold = minutesThreshold * 60;
   const elapsed = state.last_ts === 0 ? 0 : now - state.last_ts;
   const thresholdMet = state.count >= messagesThreshold || elapsed >= timeThreshold;
@@ -11344,12 +11372,13 @@ function handleStop(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDi
     writeState(token, { count: state.count, last_ts: state.last_ts, last_stop_nn: state.last_stop_nn }, tmpDir);
     return;
   }
-  const nextNn = String(Number(state.last_stop_nn) + 1).padStart(2, "0");
   const date = formatDate(now);
+  const maxNn = maxCheckpointNnSync(vaultRoot, date, token, logsFolder);
+  const nextNn = String(maxNn + 1).padStart(2, "0");
+  const since = maxNn === 0 ? " since start" : ` since checkpoint-${String(maxNn).padStart(2, "0")}`;
   const filename = `${date}-${token}-checkpoint-${nextNn}.md`;
-  const since = state.last_stop_nn === "00" ? " since start" : ` since checkpoint-${state.last_stop_nn}`;
   emitBlock(`${filename}${since}`);
-  writeState(token, { count: 0, last_ts: now, last_stop_nn: nextNn }, tmpDir);
+  writeState(token, { count: 0, last_ts: now, last_stop_nn: nextNn, pending_stub: state.pending_stub }, tmpDir);
 }
 var PRECOMPACT_STUB_TEMPLATE = (date, nn) => `---
 tags: [checkpoint, session-log]
@@ -11388,10 +11417,11 @@ async function handlePrecompact(token, vaultRoot, now = Math.floor(Date.now() /
   if (state.last_ts > 0 && now - state.last_ts < PRECOMPACT_RECENCY) {
     return;
   }
-  const stubNn = String(Number(state.last_stop_nn) + 1).padStart(2, "0");
+  if (state.pending_stub) {
+    return;
+  }
   const date = formatDate(now);
-  const stubFilename = `${date}-${token}-checkpoint-${stubNn}.md`;
-  let logsFolder = "07-logs";
+  let logsFolder = DEFAULT_LOGS_FOLDER;
   try {
     const config = await loadVaultConfig(vaultRoot);
     logsFolder = config.folders.logs;
@@ -11399,6 +11429,16 @@ async function handlePrecompact(token, vaultRoot, now = Math.floor(Date.now() /
   const yyyy = formatYYYY(now);
   const mm = formatMM(now);
   const stubDir = join7(vaultRoot, logsFolder, yyyy, mm);
+  const existingFiles = await readdir2(stubDir).catch(() => []);
+  const prefix = `${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-${stubNn}.md`;
   const stubPath = join7(stubDir, stubFilename);
   try {
     await mkdir4(stubDir, { recursive: true });
@@ -11415,15 +11455,79 @@ async function handlePrecompact(token, vaultRoot, now = Math.floor(Date.now() /
     pending_stub: stubFilename
   }, tmpDir);
 }
-function handlePostcompact(token, _now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
+function handlePostcompact(token, vaultRoot, now = Math.floor(Date.now() / 1000), tmpDir = osTmpdir()) {
   const state = readState(token, tmpDir);
   if (!state.pending_stub) {
     writeState(token, { count: 0, last_ts: state.last_ts, last_stop_nn: state.last_stop_nn }, tmpDir);
     return;
   }
-  const since = state.last_stop_nn === "00" ? " since start" : ` since checkpoint-${state.last_stop_nn}`;
+  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: 0, last_stop_nn: state.last_stop_nn }, tmpDir);
+  writeState(token, { count: 0, last_ts: now, last_stop_nn: stubNn }, 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);
 }
 async function checkpointCommand(mode, token, vaultRoot) {
   try {
@@ -11435,7 +11539,7 @@ async function checkpointCommand(mode, token, vaultRoot) {
         await handlePrecompact(token, vaultRoot);
         break;
       case "postcompact":
-        handlePostcompact(token);
+        postcompactFallback(token, vaultRoot);
         break;
       case "reset":
         handleReset(token);
@@ -11451,7 +11555,7 @@ async function checkpointCommand(mode, token, vaultRoot) {
 }
 
 // src/internal/migrate.ts
-import { readFile as readFile5, readdir as readdir2, writeFile as writeFile6 } from "node:fs/promises";
+import { readFile as readFile5, readdir as readdir3, writeFile as writeFile6 } from "node:fs/promises";
 import { join as join8 } from "node:path";
 init_dist();
 function parseFrontmatterWithRest(rawText) {
@@ -11480,7 +11584,7 @@ function parseFrontmatterWithRest(rawText) {
 }
 async function listMdFiles(dir) {
   try {
-    const entries = await readdir2(dir);
+    const entries = await readdir3(dir);
     return entries.filter((e2) => e2.endsWith(".md"));
   } catch {
     return [];
@@ -11492,7 +11596,7 @@ async function runBackfillRecapped(logsFolder) {
   let skipped = 0;
   let yearDirs = [];
   try {
-    yearDirs = await readdir2(logsFolder);
+    yearDirs = await readdir3(logsFolder);
   } catch {
     return { backfilled: 0, skipped: 0 };
   }
@@ -11500,7 +11604,7 @@ async function runBackfillRecapped(logsFolder) {
     const yearPath = join8(logsFolder, yearDir);
     let monthDirs = [];
     try {
-      monthDirs = await readdir2(yearPath);
+      monthDirs = await readdir3(yearPath);
     } catch {
       continue;
     }
@@ -11563,7 +11667,7 @@ async function migrateCommand(migrationName) {
 
 // src/internal/orphan-scan.ts
 init_dist();
-import { readFile as readFile6, readdir as readdir3 } from "node:fs/promises";
+import { readFile as readFile6, readdir as readdir4 } from "node:fs/promises";
 import { join as join9 } from "node:path";
 function parseFrontmatter(rawText) {
   const text = rawText.replace(/\r\n/g, `
@@ -11592,7 +11696,7 @@ function getMonthParts(now = new Date) {
 }
 async function listMdFiles2(dir) {
   try {
-    const entries = await readdir3(dir);
+    const entries = await readdir4(dir);
     return entries.filter((e2) => e2.endsWith(".md"));
   } catch {
     return [];
@@ -12115,7 +12219,7 @@ import {
   mkdir as mkdir6,
   mkdtemp as mkdtemp2,
   readFile as readFile8,
-  readdir as readdir4,
+  readdir as readdir5,
   rename as rename6,
   rm as rm2,
   stat as stat4,
@@ -12156,7 +12260,7 @@ async function extractTarball2(tarball, destDir) {
     throw new Error(`tar extraction failed (exit ${exitCode}): ${errText.trim()}`);
   }
   await unlink3(tarPath);
-  const entries = await readdir4(destDir);
+  const entries = await readdir5(destDir);
   const topLevel = entries.find((e2) => e2 !== "bundle.tar.gz");
   if (!topLevel) {
     throw new Error("Extracted tarball contains no top-level directory");
@@ -12170,7 +12274,7 @@ async function listFilesRecursive2(dir) {
     const current = queue.pop();
     let entries;
     try {
-      entries = await readdir4(current);
+      entries = await readdir5(current);
     } catch {
       continue;
     }
@@ -12395,7 +12499,7 @@ async function cleanPluginCache2(installedPluginsPath, installedPluginsCacheDir)
   } catch {}
   if (onebrainDirs.length === 0) {
     try {
-      const marketplaceDirs = await readdir4(cacheDir);
+      const marketplaceDirs = await readdir5(cacheDir);
       for (const mp of marketplaceDirs) {
         const candidate = join12(cacheDir, mp, "onebrain");
         try {
@@ -12411,7 +12515,7 @@ async function cleanPluginCache2(installedPluginsPath, installedPluginsCacheDir)
   for (const pluginDir of onebrainDirs) {
     let versionDirs;
     try {
-      versionDirs = await readdir4(pluginDir);
+      versionDirs = await readdir5(pluginDir);
     } catch {
       continue;
     }
@@ -12598,7 +12702,7 @@ async function vaultSyncCommand2(vaultRoot, opts = {}) {
 }
 
 // src/index.ts
-var VERSION = "2.0.2";
+var VERSION = "2.0.4";
 var RELEASE_DATE = "2026-04-25";
 var VERSION_STRING = `OneBrain v${VERSION} \u2014 released ${RELEASE_DATE}`;
 if (process.argv.slice(2).length === 0) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@onebrain-ai/cli",
-  "version": "2.0.2",
+  "version": "2.0.4",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",