@onebrain-ai/cli 2.1.16 → 2.2.1

package/README.md

@@ -198,7 +198,7 @@ OneBrain has automatic behaviors that run without you doing anything:
 
 **The practical result:** Just say "bye" and everything is saved. If the session ends unexpectedly, you lose at most 15 messages — the last checkpoint recovers the rest.
 
-> Auto Checkpoint requires Claude Code (uses the Claude Code stop hook) and the `onebrain` CLI binary. Install with `npm install -g @onebrain-ai/cli`. Auto Session Summary works with any agent that follows INSTRUCTIONS.md.
+> Auto Checkpoint runs on Claude Code (`Stop` hook) and Gemini CLI (`AfterAgent` hook), and uses the `onebrain` CLI binary. Install with `npm install -g @onebrain-ai/cli`. Auto Session Summary works with any agent that follows INSTRUCTIONS.md.
 
 ---
 
@@ -214,7 +214,7 @@ OneBrain doesn't just store markdown. Every feature exists to make you and the a
 | 📂 | **Vault-native Markdown** | Plain Markdown, no lock-in. Your data stays yours forever |
 | 🔀 | **Multi-Harness OS** | Switch between Claude Code, Gemini CLI, Codex, Qwen, or BYO LLM — context never breaks. [See architecture ↑](#the-harness-os-architecture) |
 | 🔌 | **Zero Config** | Clone, open in Obsidian, run `/onboarding`. Ready in under 2 minutes |
-| 📓 | **Session Logs & Checkpoints** | Every conversation saved with summaries and action items. Auto-checkpoints fire every 15 messages or 30 min so nothing is lost mid-session *(auto-checkpoint requires Claude Code)* |
+| 📓 | **Session Logs & Checkpoints** | Every conversation saved with summaries and action items. Auto-checkpoints fire every 15 messages or 30 min so nothing is lost mid-session *(supported on Claude Code and Gemini CLI)* |
 | 💾 | **Auto Session Summary** | When you say "bye", the agent silently saves a complete session log — no `/wrapup` needed |
 | 🔗 | **Knowledge Synthesis** | `/consolidate` turns inbox captures into permanent connected knowledge |
 | 🔬 | **Confidence-scored Memory** | Every insight carries `[conf:high/medium/low]` + `[verified:YYYY-MM-DD]` — knowledge that grows more reliable with use |
@@ -276,7 +276,7 @@ Each harness reads OneBrain's instruction file automatically. Install it, run it
 | **OpenAI Codex** | `npm install -g @openai/codex` | `codex` | `AGENTS.md` |
 | **Qwen Code** | `npm install -g @qwen-code/qwen-code` | `qwen` | `AGENTS.md` |
 
-> Auto-checkpoint and the Stop hook are wired up for Claude Code today. The other harnesses get the rest of the skill surface (24+ commands) immediately, and gain hook coverage as upstream support lands.
+> Auto-checkpoint and stop-hook coverage ship for Claude Code (`Stop` + optional `PostToolUse` qmd) and Gemini CLI (`AfterAgent` + optional `AfterTool` qmd) out of the box. Slash commands are namespaced on Gemini (`/onebrain:braindump`) to avoid collisions with built-ins; on Claude they invoke directly (`/braindump`). Other harnesses gain hook coverage as upstream support lands.
 
 ### 1. Install the OneBrain CLI
 
@@ -342,7 +342,7 @@ Same vault. Same skills. Same memory. The LLM swaps; OneBrain doesn't notice.
 
 ## 📋 24+ Commands
 
-The full skill surface, alphabetized by workflow.
+The full skill surface, alphabetized by workflow. **Gemini CLI users:** prepend the `onebrain:` namespace, e.g. `/onebrain:braindump` instead of `/braindump` (avoids collisions with Gemini built-in commands like `/help` and `/tasks`).
 
 | Command | What it does |
 |---------|-------------|
@@ -402,7 +402,8 @@ onebrain/
 ├── GEMINI.md          Instructions for Gemini CLI
 ├── AGENTS.md          Universal agent instructions
 ├── vault.yml          Your vault configuration (created during onboarding)
-└── .claude/plugins/   AI skills and hooks
+├── .claude/plugins/   AI skills, hooks, and shared INSTRUCTIONS (read by Claude Code)
+└── .gemini/           Gemini CLI project config — hooks + namespaced slash commands
 ```
 
 The core workflow: capture everything to inbox → process with `/consolidate` → synthesize into knowledge or save as reference → archive what's done.

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: "2.1.16",
+    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",
@@ -10205,20 +10207,6 @@ function applyPermissions(settings) {
   }
   return added;
 }
-async function registerGeminiHooks(vaultRoot) {
-  const geminiSettingsPath = join4(vaultRoot, ".gemini", "settings.json");
-  try {
-    const text = await readFile(geminiSettingsPath, "utf8");
-    const settings = JSON.parse(text);
-    applyHooks(settings);
-    await writeSettings(geminiSettingsPath, settings);
-  } catch (err) {
-    if (err.code !== "ENOENT") {
-      process.stderr.write(`register-hooks: gemini warning: ${err instanceof Error ? err.message : String(err)}
-`);
-    }
-  }
-}
 async function registerDirectPath() {
   const home = homedir();
   const candidates = [join4(home, ".zshrc"), join4(home, ".bashrc"), join4(home, ".profile")];
@@ -10316,9 +10304,6 @@ async function runRegisterHooks(opts = {}) {
       if (!isTTY)
         note("permissions ok");
     }
-    if (harness === "gemini") {
-      await registerGeminiHooks(vaultRoot);
-    }
     if (harness === "direct") {
       await registerDirectPath();
     }
@@ -10495,6 +10480,43 @@ async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink2) {
   }
   return { filesAdded, filesRemoved };
 }
+async function syncGeminiConfig(extractedDir, vaultRoot, unlinkFn = unlink2) {
+  const sourceGemini = join5(extractedDir, ".gemini");
+  const destGemini = join5(vaultRoot, ".gemini");
+  try {
+    await stat4(sourceGemini);
+  } catch {
+    return { filesAdded: 0, filesRemoved: 0 };
+  }
+  await mkdirIdempotent(destGemini);
+  const sourceFiles = await listFilesRecursive(sourceGemini);
+  const sourceRelSet = new Set(sourceFiles.map((f2) => relative(sourceGemini, f2)));
+  const destFiles = await listFilesRecursive(destGemini);
+  const destRelSet = new Set(destFiles.map((f2) => relative(destGemini, f2)));
+  const staleRels = [];
+  for (const rel of destRelSet) {
+    if (!sourceRelSet.has(rel))
+      staleRels.push(rel);
+  }
+  let filesAdded = 0;
+  for (const srcPath of sourceFiles) {
+    const rel = relative(sourceGemini, srcPath);
+    const destPath = join5(destGemini, rel);
+    await mkdirIdempotent(dirname2(destPath));
+    const content = await readFile2(srcPath);
+    await writeFile3(destPath, content);
+    filesAdded++;
+  }
+  let filesRemoved = 0;
+  for (const rel of staleRels) {
+    const destPath = join5(destGemini, rel);
+    try {
+      await unlinkFn(destPath);
+      filesRemoved++;
+    } catch {}
+  }
+  return { filesAdded, filesRemoved };
+}
 async function copyRootDocs(extractedDir, vaultRoot) {
   const docs = ["CONTRIBUTING.md", "CHANGELOG.md", "PLUGIN-CHANGELOG.md"];
   for (const doc of docs) {
@@ -10821,9 +10843,10 @@ async function runVaultSync(vaultRoot, opts = {}) {
     stopSpinner(`onebrain-ai/onebrain@${branch} (v${result.version})`);
     startSpinner("\uD83D\uDCC2", "Syncing files");
     try {
-      const { filesAdded, filesRemoved } = await syncPluginFiles(extractedDir, vaultRoot, unlinkFn);
-      result.filesAdded = filesAdded;
-      result.filesRemoved = filesRemoved;
+      const pluginResult = await syncPluginFiles(extractedDir, vaultRoot, unlinkFn);
+      const geminiResult = await syncGeminiConfig(extractedDir, vaultRoot, unlinkFn);
+      result.filesAdded = pluginResult.filesAdded + geminiResult.filesAdded;
+      result.filesRemoved = pluginResult.filesRemoved + geminiResult.filesRemoved;
     } catch (err) {
       stopSpinner("plugin sync failed");
       const msg = err instanceof Error ? err.message : String(err);
@@ -10968,7 +10991,7 @@ var import_picocolors5 = __toESM(require_picocolors(), 1);
 var import_picocolors = __toESM(require_picocolors(), 1);
 function resolveBinaryVersion() {
   if (true)
-    return "2.1.16";
+    return "2.2.1";
   try {
     const pkg = require_package();
     return pkg.version ?? "dev";
@@ -11460,7 +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);
@@ -12582,9 +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, `
 `);
@@ -12618,6 +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"));
@@ -12632,10 +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)
@@ -12652,32 +12743,51 @@ async function scanMonthDir(monthDir, currentToken, today, seenTokens) {
       continue;
     if (ftoken === currentToken)
       continue;
-    if (seenTokens.has(ftoken))
-      continue;
-    if (await hasManualSessionLog(monthDir, fdate))
+    if (await dateHasManualLog(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)}
 `);
 }
@@ -13199,8 +13309,8 @@ function patchUtf8(stream) {
 }
 
 // src/index.ts
-var VERSION = "2.1.16";
-var RELEASE_DATE = "2026-05-06";
+var VERSION = "2.2.1";
+var RELEASE_DATE = "2026-05-07";
 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": "2.1.16",
+  "version": "2.2.1",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",