@onebrain-ai/cli 2.2.3 → 2.2.5

package/README.md

@@ -23,7 +23,7 @@
 </p>
 
 <p align="center">
-  <strong>Your personal AI OS</strong> — persistent memory, 24+ skills, and a full local stack<br>
+  <strong>Your personal AI OS</strong> — persistent memory, 25+ skills, and a full local stack<br>
   (Claude Code + Obsidian + tmux + Telegram), entirely on your own machine.
 </p>
 
@@ -35,7 +35,7 @@
 
 ## What is OneBrain?
 
-OneBrain is an AI operating system layer built on top of Obsidian. It gives your AI agent persistent memory, a structured knowledge vault, and 24+ pre-built skills — so every session picks up exactly where the last one left off.
+OneBrain is an AI operating system layer built on top of Obsidian. It gives your AI agent persistent memory, a structured knowledge vault, and 25+ pre-built skills — so every session picks up exactly where the last one left off.
 
 Unlike chat-based AI tools, OneBrain lives in plain Markdown files you own forever. No cloud sync required. No proprietary format. Just your agent, your vault, your data.
 
@@ -70,7 +70,7 @@ OneBrain doesn't compete with Claude Code, Gemini CLI, or any other AI harness
 
 | # | Layer | Role | What lives here |
 |---|---|---|---|
-| 01 | **OneBrain** | OS layer (plugin + CLI) | 24+ skills · lifecycle hooks · vault sync · indexing · checkpoints · harness routing |
+| 01 | **OneBrain** | OS layer (plugin + CLI) | 25+ skills · lifecycle hooks · vault sync · indexing · checkpoints · harness routing |
 | 02 | **Harness** | Agentic runtime | Bring your own — Claude Code · Gemini CLI · Codex · Qwen · ... |
 | 03 | **LLM** | Intelligence source | Local (mlx, ollama) · cloud (claude, gemini, gpt) · raw API |
 | 04 | **Obsidian Vault** | Source of truth | Plain Markdown — notes, memory, decisions, knowledge graph |
@@ -84,7 +84,7 @@ A great harness already knows how to talk to an LLM, edit files, and run shell c
 | | What OneBrain adds | Why it matters |
 |---|---|---|
 | 🧠 | **Memory** — Identity, preferences, decisions, project state — promoted across four tiers as it earns trust | The harness alone starts every session from zero. OneBrain doesn't. |
-| ⚡ | **Skills** — 24+ vault-aware verbs (`/braindump`, `/research`, `/distill`, `/learn`, `/wrapup`, …) | Pre-built workflows the harness would otherwise need you to script every time. |
+| ⚡ | **Skills** — 25+ vault-aware verbs (`/braindump`, `/research`, `/distill`, `/learn`, `/wrapup`, …) | Pre-built workflows the harness would otherwise need you to script every time. |
 | 🎯 | **Calibration** — Every correction, every preference, every learned habit tunes the agent to *you* | The longer you use it, the sharper it gets — your vault is the training data. |
 | 🔀 | **Continuity** — Context lives in the vault, not the harness | Switch from Claude Code to Gemini CLI to Codex. Same memory. Same skills. Same agent. |
 
@@ -210,7 +210,7 @@ OneBrain doesn't just store markdown. Every feature exists to make you and the a
 |---|---|---|
 | 🧠 | **Persistent Memory** | Remembers your name, goals, preferences, and decisions across every session |
 | 🖥️ | **Personal AI OS** | Full local stack: Claude Code + Obsidian + tmux + Telegram — no cloud infra needed |
-| ⚡ | **24+ Skills** | Braindump, research, consolidate, bookmark, import files, daily briefing, and more |
+| ⚡ | **25+ Skills** | Braindump, research, consolidate, bookmark, import files, daily briefing, and more |
 | 📂 | **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 |
@@ -340,37 +340,55 @@ Same vault. Same skills. Same memory. The LLM swaps; OneBrain doesn't notice.
 
 <a id="commands"></a>
 
-## 📋 24+ Commands
+## 📋 25+ Commands
 
-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`).
+Skills are organized by workflow phase. **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`).
+
+### 📥 INPUT — Capture & ingest
 
 | Command | What it does |
 |---------|-------------|
-| `/onboarding` | First-run setup — run this first |
+| `/onboarding` | First-run setup — run this first · *first run only* |
 | `/braindump` | Dump everything on your mind — it gets classified and filed |
 | `/capture` | Quick note with auto-linking to related notes |
 | `/bookmark [url]` | Save a URL with AI-generated name, description, and category to Bookmarks.md |
-| `/consolidate` | Process inbox into permanent knowledge |
-| `/connect` | Find connections between notes, suggest wikilinks |
-| `/research [topic]` | Web research → structured note in your vault |
 | `/summarize [url]` | Fetch a URL and save a deep summary note |
 | `/import [path]` | Import local files (PDF, Word, images, scripts) into vault notes |
 | `/reading-notes` | Turn a book or article into structured notes |
+| `/research [topic]` | Web research → structured note in your vault |
+
+### ⚙️ PROCESS — Synthesize & organize
+
+| Command | What it does |
+|---------|-------------|
+| `/consolidate` | Process inbox into permanent knowledge |
+| `/distill [topic]` | Crystallize a completed topic thread into a permanent knowledge note in `03-knowledge/` |
+| `/connect` | Find connections between notes, suggest wikilinks |
+| `/recap` | Cross-session synthesis — batch-promote recurring insights from session logs into `memory/` files (does NOT write to MEMORY.md) |
 | `/weekly` | Review the week, surface patterns, set intentions |
 | `/daily` | Daily briefing — surfaces tasks and last session context, then saves your focus as a daily note |
-| `/recap` | Cross-session synthesis — batch-promote recurring insights from session logs into `memory/` files (does NOT write to MEMORY.md) |
-| `/distill [topic]` | Crystallize a completed topic thread into a permanent knowledge note in `03-knowledge/` |
+| `/learn` | Teach the agent something — facts about your world or behavioral preferences |
+
+### 🔍 RECALL — Retrieve & navigate
+
+| Command | What it does |
+|---------|-------------|
+| `/search` | General vault retrieval — answers what + why questions across MEMORY, sessions, plans, decisions logs, notes |
 | `/tasks` | Live task dashboard in Obsidian — creates/updates `TASKS.md` with always-current query sections |
 | `/moc` | Vault portal in Obsidian — creates/updates `MOC.md` with projects, areas, knowledge, tasks, and pinned links |
-| `/wrapup` | Wrap up session — merges any auto-checkpoints and saves full summary to session log |
-| `/learn` | Teach the agent something — facts about your world or behavioral preferences |
 | `/memory-review` | Interactive review of memory files — keep, update, deprecate, or delete entries |
-| `/clone` | Package your agent context for transfer to a new vault |
+
+### 🔧 MAINTAIN — System housekeeping
+
+| Command | What it does |
+|---------|-------------|
+| `/update` | Update skills, config, and plugins from GitHub |
+| `/doctor` | Vault + config health check — broken links, orphan notes, stale memory entries, inbox backlog |
 | `/reorganize` | Migrate flat notes into organized subfolders |
+| `/clone` | Package your agent context for transfer to a new vault |
 | `/qmd` | Set up fast vault search index — enables semantic search across all notes |
-| `/doctor` | Vault + config health check — broken links, orphan notes, stale memory entries, inbox backlog |
-| `/update` | Update skills, config, and plugins from GitHub |
 | `/help` | List all available commands with descriptions |
+| `/wrapup` | Wrap up session — merges any auto-checkpoints and saves full summary to session log |
 
 <details>
 <summary><strong>📁 Vault Structure</strong></summary>

package/dist/onebrain

@@ -9560,7 +9560,7 @@ var init_lib = __esm(() => {
 var require_package = __commonJS((exports, module) => {
   module.exports = {
     name: "@onebrain-ai/cli",
-    version: "2.2.3",
+    version: "2.2.5",
     description: "CLI for OneBrain \u2014 personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
     keywords: [
       "onebrain",
@@ -10015,23 +10015,30 @@ async function pathExists(p2) {
     return false;
   }
 }
-async function detectHarness(vaultRoot) {
+async function detectHarnesses(vaultRoot) {
   const env = process.env["ONEBRAIN_HARNESS"];
   if (env) {
     if (env === "claude" || env === "claude-code")
-      return "claude";
+      return ["claude"];
     if (env === "gemini")
-      return "gemini";
+      return ["gemini"];
     if (env === "direct")
-      return "direct";
+      return ["direct"];
     process.stderr.write(`harness: unknown ONEBRAIN_HARNESS value "${env}" \u2014 ignoring, falling back to directory detection
 `);
   }
-  if (await pathExists(join3(vaultRoot, ".gemini")))
-    return "gemini";
+  const detected = [];
   if (await pathExists(join3(vaultRoot, ".claude")))
-    return "claude";
-  return "direct";
+    detected.push("claude");
+  if (await pathExists(join3(vaultRoot, ".gemini")))
+    detected.push("gemini");
+  if (detected.length === 0)
+    return ["direct"];
+  return detected;
+}
+async function detectHarness(vaultRoot) {
+  const [first] = await detectHarnesses(vaultRoot);
+  return first ?? "direct";
 }
 var init_harness = () => {};
 
@@ -10060,13 +10067,34 @@ async function writeSettings(settingsPath, settings) {
   await writeFile2(tmpPath, JSON.stringify(settings, null, 4), "utf8");
   await rename2(tmpPath, settingsPath);
 }
-function checkHookPresence(groups, targetCmd) {
+function matchesSpec(entry, spec) {
+  const fullCmd = [spec.command, ...spec.args].join(" ");
+  if (entry.command === spec.command && JSON.stringify(entry.args ?? []) === JSON.stringify(spec.args)) {
+    return true;
+  }
+  if (entry.command === fullCmd && !entry.args) {
+    return true;
+  }
+  return false;
+}
+function rewriteIfShellForm(entry, spec) {
+  const fullCmd = [spec.command, ...spec.args].join(" ");
+  if (entry.command === fullCmd && !entry.args) {
+    entry.command = spec.command;
+    entry.args = [...spec.args];
+    if (!entry.type)
+      entry.type = "command";
+    return true;
+  }
+  return false;
+}
+function checkHookPresence(groups, spec) {
   let foundMigrate = false;
   for (const group of groups) {
     for (const entry of group.hooks ?? []) {
-      const cmd = entry.command ?? "";
-      if (cmd === targetCmd)
+      if (matchesSpec(entry, spec))
         return "found";
+      const cmd = entry.command ?? "";
       if (cmd.includes("checkpoint-hook.sh"))
         foundMigrate = true;
     }
@@ -10096,22 +10124,30 @@ function applyHooks(settings) {
     }
   }
   for (const event of HOOK_EVENTS) {
-    const cmd = HOOK_COMMANDS[event];
-    if (!cmd)
+    const spec = HOOK_SPECS[event];
+    if (!spec)
       continue;
     if (!hooks[event])
       hooks[event] = [];
     const groups = hooks[event];
-    const presence = checkHookPresence(groups, cmd);
+    let rewroteShellForm = false;
+    for (const group of groups) {
+      for (const entry of group.hooks ?? []) {
+        if (rewriteIfShellForm(entry, spec))
+          rewroteShellForm = true;
+      }
+    }
+    const presence = checkHookPresence(groups, spec);
     if (presence === "found") {
-      result[event] = "ok";
+      result[event] = rewroteShellForm ? "migrated" : "ok";
     } else if (presence === "migrate") {
       for (const group of groups) {
         if (group.matcher === undefined)
           group.matcher = "";
         for (const entry of group.hooks ?? []) {
           if ((entry.command ?? "").includes("checkpoint-hook.sh")) {
-            entry.command = cmd;
+            entry.command = spec.command;
+            entry.args = [...spec.args];
             if (!entry.type)
               entry.type = "command";
           }
@@ -10119,12 +10155,18 @@ function applyHooks(settings) {
       }
       result[event] = "migrated";
     } else {
-      groups.push({ matcher: "", hooks: [{ type: "command", command: cmd }] });
+      groups.push({
+        matcher: "",
+        hooks: [{ type: "command", command: spec.command, args: [...spec.args] }]
+      });
       result[event] = "added";
     }
   }
   return result;
 }
+function isCanonicalQmdEntry(entry) {
+  return matchesSpec(entry, QMD_SPEC);
+}
 function isLegacyQmdCmd(cmd) {
   return /\bqmd\s+update\b/.test(cmd);
 }
@@ -10137,7 +10179,8 @@ function migrateLegacyQmdEntries(groups, keepCanonical) {
       let groupTouched = false;
       for (const entry of group.hooks) {
         if (isLegacyQmdCmd(entry.command ?? "")) {
-          entry.command = QMD_CMD;
+          entry.command = QMD_SPEC.command;
+          entry.args = [...QMD_SPEC.args];
           if (!entry.type)
             entry.type = "command";
           groupTouched = true;
@@ -10151,20 +10194,26 @@ function migrateLegacyQmdEntries(groups, keepCanonical) {
       const before = group.hooks.length;
       group.hooks = group.hooks.filter((h) => {
         const cmd = h.command ?? "";
-        return !isLegacyQmdCmd(cmd) && cmd !== QMD_CMD;
+        return !isLegacyQmdCmd(cmd) && !isCanonicalQmdEntry(h);
       });
       if (group.hooks.length !== before)
         touched = true;
     }
   }
   if (keepCanonical) {
+    for (const group of groups) {
+      for (const entry of group.hooks ?? []) {
+        if (rewriteIfShellForm(entry, QMD_SPEC))
+          touched = true;
+      }
+    }
     let seenCanonical = false;
     for (const group of groups) {
       if (!group.hooks)
         continue;
       const before = group.hooks.length;
       group.hooks = group.hooks.filter((h) => {
-        if (h.command !== QMD_CMD)
+        if (!isCanonicalQmdEntry(h))
           return true;
         if (seenCanonical)
           return false;
@@ -10189,10 +10238,13 @@ function applyQmdHook(settings) {
     settings.hooks["PostToolUse"] = [];
   const groups = settings.hooks["PostToolUse"];
   const migrated = migrateLegacyQmdEntries(groups, true);
-  const already = groups.some((g) => g.hooks?.some((h) => h.command === QMD_CMD));
+  const already = groups.some((g) => g.hooks?.some((h) => isCanonicalQmdEntry(h)));
   if (already)
     return migrated ? "migrated" : "ok";
-  groups.push({ matcher: QMD_MATCHER, hooks: [{ type: "command", command: QMD_CMD }] });
+  groups.push({
+    matcher: QMD_MATCHER,
+    hooks: [{ type: "command", command: QMD_SPEC.command, args: [...QMD_SPEC.args] }]
+  });
   return "added";
 }
 function applyPermissions(settings) {
@@ -10237,7 +10289,7 @@ ${PATH_EXPORT}
 async function runRegisterHooks(opts = {}) {
   const vaultRoot = opts.vaultDir ?? process.cwd();
   const isTTY = opts.isTTY ?? process.stdout.isTTY ?? false;
-  const harness = await detectHarness(vaultRoot);
+  const harnesses = await detectHarnesses(vaultRoot);
   let qmdCollection;
   try {
     const vaultConfig = await loadVaultConfig(vaultRoot);
@@ -10263,52 +10315,53 @@ async function runRegisterHooks(opts = {}) {
   let hooksSpinner = null;
   let permSpinner = null;
   try {
-    if (harness === "claude") {
-      hooksSpinner = isTTY ? L2() : null;
-      hooksSpinner?.start("Registering hooks...");
-      const settings = await readSettings(settingsPath);
-      result.hooks = applyHooks(settings);
-      let qmdStatus;
-      if (qmdCollection) {
-        qmdStatus = applyQmdHook(settings);
-      } else {
-        const groups = settings.hooks?.["PostToolUse"] ?? [];
-        const stripped = migrateLegacyQmdEntries(groups, false);
-        if (stripped && groups.length === 0 && settings.hooks) {
-          delete settings.hooks["PostToolUse"];
+    for (const harness of harnesses) {
+      if (harness === "claude") {
+        hooksSpinner = isTTY ? L2() : null;
+        hooksSpinner?.start("Registering hooks...");
+        const settings = await readSettings(settingsPath);
+        result.hooks = applyHooks(settings);
+        let qmdStatus;
+        if (qmdCollection) {
+          qmdStatus = applyQmdHook(settings);
+        } else {
+          const groups = settings.hooks?.["PostToolUse"] ?? [];
+          const stripped = migrateLegacyQmdEntries(groups, false);
+          if (stripped && groups.length === 0 && settings.hooks) {
+            delete settings.hooks["PostToolUse"];
+          }
         }
+        if (isTTY) {
+          const parts = HOOK_EVENTS.map((e2) => {
+            const status = result.hooks[e2];
+            const icon = import_picocolors4.default.green(status === "ok" ? "\u2713" : status === "migrated" ? "\u2191" : "+");
+            return `${import_picocolors4.default.dim(e2)} ${icon}`;
+          });
+          if (qmdStatus) {
+            const qmdIcon = qmdStatus === "ok" ? "\u2713" : qmdStatus === "migrated" ? "\u2191" : "+";
+            parts.push(`${import_picocolors4.default.dim("PostToolUse")} ${import_picocolors4.default.green(qmdIcon)}`);
+          }
+          hooksSpinner?.stop(`Hooks  ${parts.join("  ")}`);
+        } else {
+          const hookLine = HOOK_EVENTS.map((e2) => {
+            const status = result.hooks[e2] ?? "ok";
+            return `${e2} ${status}`;
+          }).join("  ");
+          note(hookLine);
+          if (qmdStatus)
+            note(`PostToolUse ${qmdStatus}`);
+        }
+        permSpinner = isTTY ? L2() : null;
+        permSpinner?.start("Updating permissions...");
+        result.permissionsAdded = applyPermissions(settings);
+        await writeSettings(settingsPath, settings);
+        permSpinner?.stop("Permissions ok");
+        if (!isTTY)
+          note("permissions ok");
+      }
+      if (harness === "direct") {
+        await registerDirectPath();
       }
-      if (isTTY) {
-        const parts = HOOK_EVENTS.map((e2) => {
-          const status = result.hooks[e2];
-          const icon = import_picocolors4.default.green(status === "ok" ? "\u2713" : status === "migrated" ? "\u2191" : "+");
-          return `${import_picocolors4.default.dim(e2)} ${icon}`;
-        });
-        if (qmdStatus) {
-          const qmdIcon = qmdStatus === "ok" ? "\u2713" : qmdStatus === "migrated" ? "\u2191" : "+";
-          parts.push(`${import_picocolors4.default.dim("PostToolUse")} ${import_picocolors4.default.green(qmdIcon)}`);
-        }
-        hooksSpinner?.stop(`Hooks  ${parts.join("  ")}`);
-      } else {
-        const hookLine = HOOK_EVENTS.map((e2) => {
-          const status = result.hooks[e2];
-          const label = status === "ok" || status === "added" || status === "migrated" ? "ok" : status ?? "ok";
-          return `${e2} ${label}`;
-        }).join("  ");
-        note(hookLine);
-        if (qmdStatus)
-          note(`PostToolUse ${qmdStatus}`);
-      }
-      permSpinner = isTTY ? L2() : null;
-      permSpinner?.start("Updating permissions...");
-      result.permissionsAdded = applyPermissions(settings);
-      await writeSettings(settingsPath, settings);
-      permSpinner?.stop("Permissions ok");
-      if (!isTTY)
-        note("permissions ok");
-    }
-    if (harness === "direct") {
-      await registerDirectPath();
     }
     result.ok = true;
     if (!isTTY) {
@@ -10332,14 +10385,14 @@ async function registerHooksCommand(vaultDir) {
     process.exit(1);
   }
 }
-var import_picocolors4, HOOK_COMMANDS, HOOK_EVENTS, PERMISSIONS_TO_ADD, ONEBRAIN_MARKER = "# onebrain", PATH_EXPORT = 'export PATH="$HOME/.bun/bin:$HOME/.npm-global/bin:$PATH"', ALLOWED_HOOK_EVENTS2, QMD_CMD = "onebrain qmd-reindex", QMD_MATCHER = "Write|Edit";
+var import_picocolors4, HOOK_SPECS, HOOK_EVENTS, PERMISSIONS_TO_ADD, ONEBRAIN_MARKER = "# onebrain", PATH_EXPORT = 'export PATH="$HOME/.bun/bin:$HOME/.npm-global/bin:$PATH"', ALLOWED_HOOK_EVENTS2, QMD_SPEC, QMD_MATCHER = "Write|Edit";
 var init_register_hooks = __esm(() => {
   init_dist2();
   init_lib();
   init_harness();
   import_picocolors4 = __toESM(require_picocolors(), 1);
-  HOOK_COMMANDS = {
-    Stop: "onebrain checkpoint stop"
+  HOOK_SPECS = {
+    Stop: { command: "onebrain", args: ["checkpoint", "stop"] }
   };
   HOOK_EVENTS = ["Stop"];
   PERMISSIONS_TO_ADD = [
@@ -10359,6 +10412,7 @@ var init_register_hooks = __esm(() => {
     "WebSearch"
   ];
   ALLOWED_HOOK_EVENTS2 = new Set(["Stop", "PostToolUse"]);
+  QMD_SPEC = { command: "onebrain", args: ["qmd-reindex"] };
 });
 
 // src/commands/internal/vault-sync.ts
@@ -10994,7 +11048,7 @@ var import_picocolors5 = __toESM(require_picocolors(), 1);
 var import_picocolors = __toESM(require_picocolors(), 1);
 function resolveBinaryVersion() {
   if (true)
-    return "2.2.3";
+    return "2.2.5";
   try {
     const pkg = require_package();
     return pkg.version ?? "dev";
@@ -13292,8 +13346,8 @@ function patchUtf8(stream) {
 }
 
 // src/index.ts
-var VERSION = "2.2.3";
-var RELEASE_DATE = "2026-05-10";
+var VERSION = "2.2.5";
+var RELEASE_DATE = "2026-05-12";
 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": "2.2.3",
+  "version": "2.2.5",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",