@onebrain-ai/cli 2.2.0 → 2.2.1

package/dist/onebrain

@@ -8909,7 +8909,7 @@ async function loadVaultConfig(vaultRoot) {
   const file = Bun.file(vaultYmlPath);
   const exists = await file.exists();
   if (!exists) {
-    throw new Error(`vault.yml not found at ${vaultYmlPath}. Run onebrain init to set up this vault.`);
+    throw new Error(`${VAULT_YML_NOT_FOUND_PREFIX}${vaultYmlPath}. Run onebrain init to set up this vault.`);
   }
   const text = await file.text();
   const parsed = import_yaml.parse(text) ?? {};
@@ -8952,7 +8952,7 @@ async function loadVaultConfig(vaultRoot) {
   }
   return config;
 }
-var import_yaml, DEFAULT_FOLDERS, DEFAULT_CHECKPOINT;
+var import_yaml, DEFAULT_FOLDERS, DEFAULT_CHECKPOINT, VAULT_YML_NOT_FOUND_PREFIX = "vault.yml not found at ";
 var init_parser = __esm(() => {
   import_yaml = __toESM(require_dist(), 1);
   DEFAULT_FOLDERS = {
@@ -9545,7 +9545,9 @@ __export(exports_lib, {
   checkOrphanCheckpoints: () => checkOrphanCheckpoints,
   checkFolders: () => checkFolders,
   checkClaudeSettings: () => checkClaudeSettings,
-  atomicWrite: () => atomicWrite
+  atomicWrite: () => atomicWrite,
+  VAULT_YML_NOT_FOUND_PREFIX: () => VAULT_YML_NOT_FOUND_PREFIX,
+  DEFAULT_CHECKPOINT: () => DEFAULT_CHECKPOINT
 });
 var init_lib = __esm(() => {
   init_parser();
@@ -9558,7 +9560,7 @@ var init_lib = __esm(() => {
 var require_package = __commonJS((exports, module) => {
   module.exports = {
     name: "@onebrain-ai/cli",
-    version: "2.2.0",
+    version: "2.2.1",
     description: "CLI for OneBrain \u2014 personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
     keywords: [
       "onebrain",
@@ -10989,7 +10991,7 @@ var import_picocolors5 = __toESM(require_picocolors(), 1);
 var import_picocolors = __toESM(require_picocolors(), 1);
 function resolveBinaryVersion() {
   if (true)
-    return "2.2.0";
+    return "2.2.1";
   try {
     const pkg = require_package();
     return pkg.version ?? "dev";
@@ -11481,7 +11483,8 @@ async function runDoctor(opts = {}) {
       agent: "05-agent",
       archive: "06-archive",
       logs: "07-logs"
-    }
+    },
+    checkpoint: { ...DEFAULT_CHECKPOINT }
   };
   const sp1 = createStep("\uD83D\uDCCB", "vault.yml");
   const vaultYmlResult = await checkVaultYmlFn(vaultDir);
@@ -12603,9 +12606,12 @@ async function migrateCommand(migrationName, cutoffDate, vaultDir) {
 }
 
 // src/commands/internal/orphan-scan.ts
+init_parser();
 var import_yaml6 = __toESM(require_dist(), 1);
-import { readFile as readFile5, readdir as readdir4 } from "fs/promises";
+import { readFile as readFile5, readdir as readdir4, stat as stat6 } from "fs/promises";
 import { join as join9 } from "path";
+var MIN_GUARD_MINUTES = 60;
+var DEFAULT_ACTIVE_SESSION_GUARD_MS = 60 * 60 * 1000;
 function parseFrontmatter(rawText) {
   const text = rawText.replace(/\r\n/g, `
 `);
@@ -12639,6 +12645,61 @@ async function listMdFiles2(dir) {
     return [];
   }
 }
+async function getActiveSessionGuardMs(vaultRoot) {
+  try {
+    const config = await loadVaultConfig(vaultRoot);
+    const cpMinutes = config.checkpoint.minutes;
+    if (typeof cpMinutes !== "number" || !Number.isFinite(cpMinutes) || cpMinutes <= 0) {
+      return DEFAULT_ACTIVE_SESSION_GUARD_MS;
+    }
+    const minutes = Math.max(MIN_GUARD_MINUTES, 2 * cpMinutes);
+    return minutes * 60 * 1000;
+  } catch (err) {
+    const msg = err instanceof Error ? err.message : String(err);
+    const isExpectedAbsence = msg.startsWith(VAULT_YML_NOT_FOUND_PREFIX);
+    if (!isExpectedAbsence) {
+      try {
+        process.stderr.write(`onebrain orphan-scan: vault.yml unreadable, using ${MIN_GUARD_MINUTES}-min Active-Session Guard default (${msg})
+`);
+      } catch {}
+    }
+    return DEFAULT_ACTIVE_SESSION_GUARD_MS;
+  }
+}
+async function getMtimeMs(path) {
+  try {
+    const s = await stat6(path);
+    if (typeof s.mtimeMs !== "number" || !Number.isFinite(s.mtimeMs))
+      return null;
+    return s.mtimeMs;
+  } catch {
+    return null;
+  }
+}
+async function getNewestMtimeMs(filePaths) {
+  if (filePaths.length === 0)
+    return null;
+  let newest = Number.NEGATIVE_INFINITY;
+  for (const p2 of filePaths) {
+    const m3 = await getMtimeMs(p2);
+    if (m3 === null)
+      return null;
+    if (m3 > newest)
+      newest = m3;
+  }
+  return Number.isFinite(newest) ? newest : null;
+}
+async function isGroupActiveOrAmbiguous(filePaths, nowMs, guardMs) {
+  if (!Number.isFinite(guardMs) || guardMs <= 0)
+    return true;
+  const newest = await getNewestMtimeMs(filePaths);
+  if (newest === null)
+    return true;
+  const ageMs = nowMs - newest;
+  if (ageMs < 0)
+    return true;
+  return ageMs < guardMs;
+}
 async function hasManualSessionLog(monthDir, date) {
   const files = await listMdFiles2(monthDir);
   const sessionLogs = files.filter((f2) => f2.startsWith(date) && f2.includes("-session-") && f2.endsWith(".md"));
@@ -12653,10 +12714,19 @@ async function hasManualSessionLog(monthDir, date) {
   }
   return false;
 }
-async function scanMonthDir(monthDir, currentToken, today, seenTokens) {
+async function collectCandidateGroupsForMonth(monthDir, currentToken, today) {
+  const groups = new Map;
   const files = await listMdFiles2(monthDir);
   const checkpoints = files.filter((f2) => f2.includes("-checkpoint-") && f2.endsWith(".md"));
-  let count = 0;
+  const manualLogCache = new Map;
+  async function dateHasManualLog(date) {
+    const cached = manualLogCache.get(date);
+    if (cached !== undefined)
+      return cached;
+    const result = await hasManualSessionLog(monthDir, date);
+    manualLogCache.set(date, result);
+    return result;
+  }
   for (const fname of checkpoints) {
     const dateMatch = fname.match(/^(\d{4}-\d{2}-\d{2})-/);
     if (!dateMatch)
@@ -12673,32 +12743,51 @@ async function scanMonthDir(monthDir, currentToken, today, seenTokens) {
       continue;
     if (ftoken === currentToken)
       continue;
-    if (seenTokens.has(ftoken))
+    if (await dateHasManualLog(fdate))
       continue;
-    if (await hasManualSessionLog(monthDir, fdate))
-      continue;
-    seenTokens.add(ftoken);
-    count++;
+    const fpath = join9(monthDir, fname);
+    const existing = groups.get(ftoken);
+    if (existing)
+      existing.push(fpath);
+    else
+      groups.set(ftoken, [fpath]);
   }
-  return count;
+  return groups;
 }
-async function runOrphanScan(logsFolder, sessionToken, now) {
+async function runOrphanScan(logsFolder, sessionToken, now, vaultRoot) {
+  if (!vaultRoot) {
+    throw new Error("runOrphanScan: vaultRoot is required and must be a non-empty path");
+  }
   const today = `${now.getFullYear()}-${String(now.getMonth() + 1).padStart(2, "0")}-${String(now.getDate()).padStart(2, "0")}`;
   const { thisYear, thisMonth, prevYear, prevMonth } = getMonthParts(now);
   const monthDirs = [
     { year: thisYear, month: thisMonth },
     { year: prevYear, month: prevMonth }
   ];
-  const seenTokens = new Set;
-  let totalOrphans = 0;
+  const allGroups = new Map;
   for (const { year, month } of monthDirs) {
     const monthDir = join9(logsFolder, year, month);
-    totalOrphans += await scanMonthDir(monthDir, sessionToken, today, seenTokens);
+    const monthGroups = await collectCandidateGroupsForMonth(monthDir, sessionToken, today);
+    for (const [token, files] of monthGroups) {
+      const existing = allGroups.get(token);
+      if (existing)
+        existing.push(...files);
+      else
+        allGroups.set(token, [...files]);
+    }
+  }
+  const guardMs = await getActiveSessionGuardMs(vaultRoot);
+  const nowMs = now.getTime();
+  let totalOrphans = 0;
+  for (const [, files] of allGroups) {
+    if (await isGroupActiveOrAmbiguous(files, nowMs, guardMs))
+      continue;
+    totalOrphans++;
   }
   return { orphan_count: totalOrphans };
 }
 async function orphanScanCommand(logsFolder, sessionToken) {
-  const result = await runOrphanScan(logsFolder, sessionToken, new Date);
+  const result = await runOrphanScan(logsFolder, sessionToken, new Date, process.cwd());
   process.stdout.write(`${JSON.stringify(result)}
 `);
 }
@@ -13220,7 +13309,7 @@ function patchUtf8(stream) {
 }
 
 // src/index.ts
-var VERSION = "2.2.0";
+var VERSION = "2.2.1";
 var RELEASE_DATE = "2026-05-07";
 patchUtf8(process.stdout);
 patchUtf8(process.stderr);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@onebrain-ai/cli",
-  "version": "2.2.0",
+  "version": "2.2.1",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",