@onebrain-ai/cli 2.1.9 → 2.1.11

package/README.md

@@ -8,8 +8,11 @@
 <p align="center">
   <a href="https://onebrain.run"><img alt="Website" src="https://img.shields.io/badge/onebrain.run-0a0a14?style=for-the-badge&labelColor=ff2d92"></a>
   <a href="https://x.com/onebrain_run"><img alt="@onebrain_run on X" src="https://img.shields.io/badge/follow-@onebrain__run-000000?style=for-the-badge&logo=x&logoColor=white"></a>
-  <a href="https://www.npmjs.com/package/@onebrain-ai/cli"><img alt="npm" src="https://img.shields.io/npm/v/@onebrain-ai/cli?style=for-the-badge&logo=npm&color=cb3837&label=%40onebrain-ai%2Fcli"></a>
   <a href="https://github.com/onebrain-ai/onebrain/stargazers"><img alt="GitHub stars" src="https://img.shields.io/github/stars/onebrain-ai/onebrain?style=for-the-badge&color=00f3ff&logo=github"></a>
+</p>
+<p align="center">
+  <a href="https://www.npmjs.com/package/@onebrain-ai/cli"><img alt="npm" src="https://img.shields.io/npm/v/@onebrain-ai/cli?style=for-the-badge&logo=npm&color=cb3837&label=%40onebrain-ai%2Fcli"></a>
+  <a href="PLUGIN-CHANGELOG.md"><img alt="Plugin version" src="https://img.shields.io/github/package-json/v/onebrain-ai/onebrain?filename=.claude%2Fplugins%2Fonebrain%2F.claude-plugin%2Fplugin.json&style=for-the-badge&label=plugin&color=ff2d92"></a>
   <a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-MIT-7c3aed?style=for-the-badge"></a>
 </p>
 
@@ -43,129 +46,49 @@ Unlike chat-based AI tools, OneBrain lives in plain Markdown files you own forev
 - **Human → Agent** — Every preference, decision, and correction becomes persistent memory. The agent calibrates to you with every interaction.
 - **Agent → Human** — Captures, classifies, links, and synthesizes the noise of your day — so your attention stays on what only you can do.
 
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="assets/diagrams/bidir-flow-dark.svg">
+    <img alt="Bidirectional flow — Human sends preferences, decisions, and corrections to Agent; Agent returns captures, links, and synthesis. Every interaction sharpens both." src="assets/diagrams/bidir-flow-light.svg" width="640">
+  </picture>
+</p>
+
 **Harness-agnostic** — Claude Code · Gemini CLI · OpenAI Codex · Qwen · or BYO LLM via API key. [See the architecture ↓](#the-harness-os-architecture)
 
 ---
 
 ## The Harness OS Architecture
 
-OneBrain doesn't compete with Claude Code, Gemini CLI, or any other AI harness. It sits **underneath them** — the OS layer that keeps your context, memory, and skills consistent no matter which harness you're driving.
+OneBrain doesn't compete with Claude Code, Gemini CLI, or any other AI harness — **it extends them**. Whichever harness you drive, OneBrain adds the persistent memory, skill surface, and personal calibration that harnesses don't ship with. Same harness; suddenly it remembers who you are, what you're working on, and how you like to work — all while your Obsidian vault stays the durable source of truth underneath.
 
 <p align="center">
-  <img alt="OneBrain Harness OS — 5-layer architecture: Obsidian Vault, OneBrain Plugin, OneBrain CLI, Harness, LLM" src="assets/diagrams/harness-os-stack.svg" width="780">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="assets/diagrams/harness-os-stack-dark.svg">
+    <img alt="OneBrain Harness OS — 4-layer architecture: OneBrain (plugin + CLI) on top, Harness, LLM, Obsidian Vault as the source of truth at the base" src="assets/diagrams/harness-os-stack-light.svg" width="780">
+  </picture>
 </p>
 
 | # | Layer | Role | What lives here |
 |---|---|---|---|
-| 01 | **Obsidian Vault** | Cognitive interface | Plain Markdown — notes, memory, decisions, knowledge graph |
-| 02 | **OneBrain Plugin** | Skills + hooks | 24+ skills + lifecycle hooks, loaded into any harness |
-| 03 | **OneBrain CLI** | Harness orchestrator | Indexing, checkpoints, vault sync, harness routing |
-| 04 | **Harness** | Agentic runtime | Bring your own — Claude Code · Gemini CLI · Codex · Qwen · ... |
-| 05 | **LLM** | Intelligence source | Local (mlx, ollama) · cloud (claude, gemini, gpt) · raw API |
+| 01 | **OneBrain** | OS layer (plugin + CLI) | 24+ 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 |
 
 The **Harness** layer is where most AI tools pick a fight with each other. We don't — pick whichever harness you love. By familiarity, by task, or by cost. Your vault stays the same.
 
-### Pick Your Harness
-
-Each harness reads OneBrain's instruction file automatically. Install it, run it inside your vault, and the plugin loads on first prompt.
-
-| Harness | Install | Run | Reads |
-|---|---|---|---|
-| **Claude Code** *(recommended)* | `npm install -g @anthropic-ai/claude-code` | `claude` | `CLAUDE.md` |
-| **Gemini CLI** | `npm install -g @google/gemini-cli` | `gemini` | `GEMINI.md` |
-| **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.
-
-### Bring Your Own LLM (via Claude Code)
-
-Already love Claude Code? Use it as a universal frontend. Point `ANTHROPIC_BASE_URL` at any OpenAI-compatible endpoint — Claude Code stays the harness, the LLM behind it changes per task.
-
-```bash
-# Recommended: claude-code-router handles Anthropic ↔ provider translation
-npm install -g @musistudio/claude-code-router
-ccr code                                    # first-run config, then launches Claude Code via the router
-# (later) ccr stop                          # tear down the router before going native again
-
-# Or direct: point ANTHROPIC_BASE_URL at any Anthropic-protocol endpoint
-export ANTHROPIC_BASE_URL=https://your-router-or-anthropic-compatible-host
-export ANTHROPIC_API_KEY=sk-byok-key
-cd vault && claude
+### Extend, don't replace
 
-# Switch back to native Claude any time (manual-export route)
-unset ANTHROPIC_BASE_URL ANTHROPIC_API_KEY
-claude
-```
+A great harness already knows how to talk to an LLM, edit files, and run shell commands. It does **not** know who you are, what you've decided last week, or how you prefer to work. OneBrain fills exactly that gap.
 
-| Route | What it gets you |
-|---|---|
-| **Local** (mlx, ollama, llama.cpp) | Cost-free routine work, full privacy. Pair with [`litellm`](https://github.com/BerriAI/litellm) or [`claude-code-router`](https://github.com/musistudio/claude-code-router). |
-| **Cloud BYOK** (Claude, Gemini, GPT, Groq, OpenRouter) | Pay-as-you-go premium reasoning. One env-var swap, no code changes. |
-| **Hybrid** (route by task or by cost) | Cheap models for routine, premium when it counts. |
-
-Same vault. Same skills. Same memory. The LLM swaps; OneBrain doesn't notice.
-
----
-
-## Built for Synergetic Thinking
-
-OneBrain doesn't just store markdown. Every feature exists to make you and the agent better at each other's job.
-
-| | Feature | Description |
+| | What OneBrain adds | Why it matters |
 |---|---|---|
-| 🧠 | **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 |
-| 📂 | **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)* |
-| 💾 | **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 |
-| 💎 | **Knowledge Distillation** | `/distill` crystallizes a completed research thread into a permanent structured note in your knowledge base |
-| 🩺 | **Vault Doctor** | `/doctor` audits broken links, orphan notes, stale memory, and inbox backlog; `--fix` auto-repairs confidence scores and wikilinks |
-| 🎓 | **Teachable AI** | `/learn` permanently shapes how your agent thinks and responds |
-| 🪄 | **Smart Memory Review** | `/memory-review` lets you interactively prune, update, or archive memory entries one by one |
-| 🔒 | **Concurrent-session Safe** | Each session generates an isolated 6-char token — multiple parallel sessions never mix checkpoints |
-| 📱 | **Mobile Access** | Send instructions and receive briefings from anywhere via Telegram |
-| ⚙️ | **CLI Binary** | `onebrain` binary handles checkpoints, session init, doctor, vault-sync, and updates — no Bun, Python, or Node.js required |
+| 🧠 | **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. |
+| 🎯 | **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. |
 
----
-
-## Use Cases
-
-### 🖥️ Personal AI OS
-
-Run OneBrain as your personal AI operating system — a complete AI environment that runs locally with no cloud infrastructure required.
-
-**Recommended stack:**
-
-| Tool | Role |
-|------|------|
-| [Claude Code](https://claude.ai/code) | Your AI agent, running in the terminal |
-| [Obsidian](https://obsidian.md) | Your vault — single source of truth for memory and knowledge |
-| [tmux](https://github.com/tmux/tmux) | Persistent sessions that survive disconnects and reboots |
-| [Telegram](https://telegram.org) | Mobile access: send instructions, receive briefings from anywhere |
-
-**Setting up the full stack:**
-
-1. Install OneBrain and open your vault in Obsidian ([Get Started](#installation))
-2. Start a tmux session: `tmux new -s onebrain`
-3. Start Claude Code in your vault directory: `claude`
-4. Run `/telegram:configure` to connect Claude Code's built-in Telegram channel — no custom bot or external infra needed
-5. From any device, open Telegram and send instructions directly to your OneBrain agent
-
-Your agent, your vault, your data — forever.
-
-### 🧠 Thinking Partner
-
-Use OneBrain as a daily thinking partner. Capture ideas with `/braindump`, research topics with `/research`, synthesize knowledge with `/consolidate`, and surface connections you'd never find manually with `/connect`.
-
-### 📚 Knowledge Base Builder
-
-Turn your AI into a knowledge curator: research, summarize, import files, and build a connected Markdown knowledge base that grows smarter over time.
+> Pick a harness for **how it lets you work** (CLI, IDE, mobile, API). Pick OneBrain for **how it remembers you** across all of them.
 
 ---
 
@@ -177,15 +100,27 @@ Obsidian becomes your dispatch hub for everything you do:
 - **Code in repos, orchestration in vault** — agent dispatches from here to wherever the work actually lives.
 - **Markdown replaces Slack / Linear / Notion** — version-controlled, AI-readable, yours forever.
 
-The agent reaches outward FROM the vault to: **CLI / repo · website · cloud infra · social media · office docs · project notes · research · MCP servers**.
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="assets/diagrams/vault-hub-dark.svg">
+    <img alt="Obsidian as command center — eight spokes radiate from the vault to CLI/repo, website, cloud infra, social media, office docs, project notes, research, and MCP server" src="assets/diagrams/vault-hub-light.svg" width="640">
+  </picture>
+</p>
 
-No tab juggling. No tool sprawl.
+The agent reaches outward FROM the vault to every surface where the work actually lives. No tab juggling. No tool sprawl.
 
 ---
 
-## How It Works — The Path to Co-Evolution
+## The Path to Co-Evolution
 
-A tightening 3-step loop:
+A tightening 3-step loop that sharpens with every cycle.
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="assets/diagrams/coevo-loop-dark.svg">
+    <img alt="Co-Evolution loop — three nodes (01 INITIATE at top, 02 CAPTURE_INTENT at bottom-right, 03 MUTUAL_EVOLUTION at bottom-left) connected by curved arrows flowing clockwise" src="assets/diagrams/coevo-loop-light.svg" width="540">
+  </picture>
+</p>
 
 1. **Initiate** — Install the CLI, run `/onboarding`. The agent learns your name, vault, and identity. → `npm install -g @onebrain-ai/cli`
 2. **Capture intent** — Talk in natural language. The agent writes, classifies, and links in real time. → `/braindump` · `/capture` · `/bookmark`
@@ -200,9 +135,18 @@ After `/onboarding`, your AI agent:
 3. **Remembers everything** — decisions, preferences, and insights accumulate over time
 4. **Suggests next actions** — based on what's in your vault, not what it can infer from scratch
 
-### Memory System
+---
+
+## Memory System
+
+OneBrain uses a four-tier memory system — knowledge sinks downward as it gets validated, while the agent recalls upward on demand. The Semantic tier has two loading modes (always-loaded and lazy-loaded).
 
-OneBrain uses a four-tier memory system — each tier is more compressed and longer-lived than the one below. The Semantic tier has two loading modes (always-loaded and lazy-loaded):
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="assets/diagrams/memory-tiers-dark.svg">
+    <img alt="Memory tiers — four-stage persistence stack: WORKING (00-inbox + current session) at top, EPISODIC (07-logs), SEMANTIC (05-agent/MEMORY.md + memory/), and KNOWLEDGE (03-knowledge) at the base" src="assets/diagrams/memory-tiers-light.svg" width="780">
+  </picture>
+</p>
 
 | Tier | Location | What it stores | Promoted by |
 |------|----------|---------------|-------------|
@@ -212,11 +156,9 @@ OneBrain uses a four-tier memory system — each tier is more compressed and lon
 | **Semantic** (lazy-loaded) | `05-agent/memory/` | Behavioral patterns, domain facts — loaded on demand via MEMORY-INDEX.md | `/learn`, `/recap`, `/memory-review` |
 | **Knowledge** | `03-knowledge/` | Permanent synthesized notes | `/distill` |
 
----
-
-## Memory Promotion
+### Memory Promotion
 
-OneBrain organizes agent memory across three layers. Each layer has specific skills responsible for writing to it.
+Each tier has specific skills responsible for writing to it. Knowledge moves down the stack only as fast as it earns trust.
 
 | Layer | Storage | Written by |
 |---|---|---|
@@ -237,11 +179,9 @@ session → session log (`/wrapup`) → `memory/` files (`/recap`) → `MEMORY.m
 - Only behaviors applying every session with high-impact failure if missed → MEMORY.md Critical Behaviors
 - `MEMORY-INDEX.md` is loaded every session alongside `MEMORY.md` — it is the registry that enables lazy-loading of `memory/` files; updated automatically by any skill that writes to `memory/`
 
----
-
-## Automatic Session Saving
+### Automatic Session Saving
 
-OneBrain has three automatic behaviors that run without you doing anything:
+OneBrain has automatic behaviors that run without you doing anything:
 
 | Behavior | Trigger | What it does |
 |----------|---------|-------------|
@@ -262,9 +202,83 @@ OneBrain has three automatic behaviors that run without you doing anything:
 
 ---
 
+## Built for Synergetic Thinking
+
+OneBrain doesn't just store markdown. Every feature exists to make you and the agent better at each other's job.
+
+| | Feature | Description |
+|---|---|---|
+| 🧠 | **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 |
+| 📂 | **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)* |
+| 💾 | **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 |
+| 💎 | **Knowledge Distillation** | `/distill` crystallizes a completed research thread into a permanent structured note in your knowledge base |
+| 🩺 | **Vault Doctor** | `/doctor` audits broken links, orphan notes, stale memory, and inbox backlog; `--fix` auto-repairs confidence scores and wikilinks |
+| 🎓 | **Teachable AI** | `/learn` permanently shapes how your agent thinks and responds |
+| 🪄 | **Smart Memory Review** | `/memory-review` lets you interactively prune, update, or archive memory entries one by one |
+| 🔒 | **Concurrent-session Safe** | Each session generates an isolated 6-char token — multiple parallel sessions never mix checkpoints |
+| 📱 | **Mobile Access** | Send instructions and receive briefings from anywhere via Telegram |
+| ⚙️ | **CLI Binary** | `onebrain` binary handles checkpoints, session init, doctor, vault-sync, and updates — no Bun, Python, or Node.js required |
+
+---
+
+## Use Cases
+
+### 🖥️ Personal AI OS
+
+Run OneBrain as your personal AI operating system — a complete AI environment that runs locally with no cloud infrastructure required.
+
+**Recommended stack:**
+
+| Tool | Role |
+|------|------|
+| [Claude Code](https://claude.ai/code) | Your AI agent, running in the terminal |
+| [Obsidian](https://obsidian.md) | Your vault — single source of truth for memory and knowledge |
+| [tmux](https://github.com/tmux/tmux) | Persistent sessions that survive disconnects and reboots |
+| [Telegram](https://telegram.org) | Mobile access: send instructions, receive briefings from anywhere |
+
+**Setting up the full stack:**
+
+1. Install OneBrain and open your vault in Obsidian ([Get Started](#installation))
+2. Start a tmux session: `tmux new -s onebrain`
+3. Start Claude Code in your vault directory: `claude`
+4. Run `/telegram:configure` to connect Claude Code's built-in Telegram channel — no custom bot or external infra needed
+5. From any device, open Telegram and send instructions directly to your OneBrain agent
+
+Your agent, your vault, your data — forever.
+
+### 🧠 Thinking Partner
+
+Use OneBrain as a daily thinking partner. Capture ideas with `/braindump`, research topics with `/research`, synthesize knowledge with `/consolidate`, and surface connections you'd never find manually with `/connect`.
+
+### 📚 Knowledge Base Builder
+
+Turn your AI into a knowledge curator: research, summarize, import files, and build a connected Markdown knowledge base that grows smarter over time.
+
+---
+
 ## Installation
 
-### 1. Install the CLI
+### Pick Your Harness
+
+Each harness reads OneBrain's instruction file automatically. Install it, run it inside your vault, and the plugin loads on first prompt.
+
+| Harness | Install | Run | Reads |
+|---|---|---|---|
+| **Claude Code** *(recommended)* | `npm install -g @anthropic-ai/claude-code` | `claude` | `CLAUDE.md` |
+| **Gemini CLI** | `npm install -g @google/gemini-cli` | `gemini` | `GEMINI.md` |
+| **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.
+
+### 1. Install the OneBrain CLI
 
 ```bash
 npm install -g @onebrain-ai/cli
@@ -286,25 +300,49 @@ File → Open Folder as Vault → select this folder
 
 ### 4. Personalize your vault
 
-In Claude Code: `/onboarding`
+In your harness: `/onboarding`
 
 > **Adding OneBrain to an existing vault?** `cd` into it and run `onebrain init`
 
----
+### Bring Your Own LLM (via Claude Code)
 
-> **After `/update`:** Run `/reload-plugins` to pick up changes in your current session, or simply start a new session.
+Already love Claude Code? Use it as a universal frontend. Point `ANTHROPIC_BASE_URL` at any OpenAI-compatible endpoint — Claude Code stays the harness, the LLM behind it changes per task.
+
+```bash
+# Recommended: claude-code-router handles Anthropic ↔ provider translation
+npm install -g @musistudio/claude-code-router
+ccr code                                    # first-run config, then launches Claude Code via the router
+# (later) ccr stop                          # tear down the router before going native again
+
+# Or direct: point ANTHROPIC_BASE_URL at any Anthropic-protocol endpoint
+export ANTHROPIC_BASE_URL=https://your-router-or-anthropic-compatible-host
+export ANTHROPIC_API_KEY=sk-byok-key
+cd vault && claude
+
+# Switch back to native Claude any time (manual-export route)
+unset ANTHROPIC_BASE_URL ANTHROPIC_API_KEY
+claude
+```
+
+| Route | What it gets you |
+|---|---|
+| **Local** (mlx, ollama, llama.cpp) | Cost-free routine work, full privacy. Pair with [`litellm`](https://github.com/BerriAI/litellm) or [`claude-code-router`](https://github.com/musistudio/claude-code-router). |
+| **Cloud BYOK** (Claude, Gemini, GPT, Groq, OpenRouter) | Pay-as-you-go premium reasoning. One env-var swap, no code changes. |
+| **Hybrid** (route by task or by cost) | Cheap models for routine, premium when it counts. |
+
+Same vault. Same skills. Same memory. The LLM swaps; OneBrain doesn't notice.
 
 ---
 
-> **Choosing a harness?** See [The Harness OS Architecture ↑](#the-harness-os-architecture) for install commands per harness, BYO-LLM via Claude Code, and the full 5-layer stack.
+> **After `/update`:** Run `/reload-plugins` to pick up changes in your current session, or simply start a new session.
 
 ---
 
 <a id="commands"></a>
 
-<details>
-<summary><strong>📋 24+ Commands</strong></summary>
-<br>
+## 📋 24+ Commands
+
+The full skill surface, alphabetized by workflow.
 
 | Command | What it does |
 |---------|-------------|
@@ -334,8 +372,6 @@ In Claude Code: `/onboarding`
 | `/update` | Update skills, config, and plugins from GitHub |
 | `/help` | List all available commands with descriptions |
 
-</details>
-
 <details>
 <summary><strong>📁 Vault Structure</strong></summary>
 <br>
@@ -403,28 +439,9 @@ Checkpoints: `07-logs/YYYY/MM/YYYY-MM-DD-{session_token}-checkpoint-NN.md` — a
 
 </details>
 
-<details>
-<summary><strong>🧠 Memory System</strong></summary>
-<br>
-
-OneBrain uses a four-tier memory system, where knowledge flows upward as it gets validated. The Semantic tier has two loading modes (always-loaded and lazy-loaded):
+## Task Syntax
 
-**Tier 1 — Working memory** (`00-inbox/` + current session)
-Everything that hasn't been processed yet. Captures from `/braindump`, `/capture`, and quick notes land here. Process with `/consolidate` to move into the knowledge base.
-
-**Tier 2 — Episodic memory** (`07-logs/`)
-Session logs: `YYYY-MM-DD-session-NN.md` in `YYYY/MM/` subfolders. Contains summaries, decisions, insights, and action items from each session. Generated by `/wrapup`.
-Checkpoints: `YYYY-MM-DD-{session_token}-checkpoint-NN.md` — auto-generated mid-session by hooks. Incorporated and deleted by `/wrapup`.
-
-**Tier 3 — Semantic memory** (`05-agent/MEMORY.md` + `05-agent/MEMORY-INDEX.md` + `05-agent/memory/`)
-Always loaded at session start: `MEMORY.md` holds Identity, Active Projects, and Critical Behaviors (~55 lines target). `MEMORY-INDEX.md` is the registry of all `memory/` files — loaded every session, enables lazy-loading. Individual `memory/` files are lazy-loaded on demand via MEMORY-INDEX.md. Only `/learn` writes to MEMORY.md Critical Behaviors. Use `/doctor --fix` to audit and repair stale entries.
-
-**Tier 4 — Knowledge base** (`03-knowledge/`)
-Permanent, synthesized notes. `/distill` crystallizes a completed topic thread into a structured note in `03-knowledge/`.
-
-### Task Syntax
-
-OneBrain uses the [Obsidian Tasks](https://publish.obsidian.md/tasks/) plugin format:
+OneBrain creates tasks in [Obsidian Tasks](https://publish.obsidian.md/tasks/) plugin format:
 
 ```
 - [ ] Task description 📅 2026-03-25
@@ -433,7 +450,7 @@ OneBrain uses the [Obsidian Tasks](https://publish.obsidian.md/tasks/) plugin fo
 
 Tasks live inline in your notes — the Tasks plugin surfaces them across the vault. Run `/tasks` to open a live dashboard in Obsidian (`TASKS.md` at vault root) with sections for overdue, due this week, unscheduled, due later, and recently completed.
 
-</details>
+---
 
 ## OneBrain Cloud
 

package/dist/onebrain

@@ -9268,6 +9268,10 @@ async function checkVaultYmlKeys(vaultRoot) {
     if (raw[key] === undefined)
       errors.push(`missing key: ${key}`);
   }
+  for (const key of SOFT_REQUIRED_VAULT_YML_KEYS) {
+    if (raw[key] === undefined)
+      warnings.push(`missing key: ${key}`);
+  }
   const folders = raw["folders"] ?? {};
   for (const key of REQUIRED_FOLDER_KEYS) {
     if (folders[key] === undefined)
@@ -9305,8 +9309,16 @@ async function checkVaultYmlKeys(vaultRoot) {
     };
   }
   if (warnings.length > 0) {
-    const fixableWarnings = warnings.filter((w) => w.includes("onebrain_version") || w.includes("method") || w.includes("runtime.harness"));
-    const hint = fixableWarnings.length > 0 ? "Run onebrain doctor --fix to remove deprecated keys" : undefined;
+    const hasDeprecated = warnings.some((w) => w.includes("onebrain_version") || w.includes("method") || w.includes("runtime.harness"));
+    const hasMissingSoftKey = warnings.some((w) => w.startsWith("missing key:"));
+    let hint;
+    if (hasMissingSoftKey && hasDeprecated) {
+      hint = "Run onebrain doctor --fix to repair vault.yml";
+    } else if (hasMissingSoftKey) {
+      hint = "Run onebrain doctor --fix to backfill defaults";
+    } else if (hasDeprecated) {
+      hint = "Run onebrain doctor --fix to remove deprecated keys";
+    }
     return {
       check: "vault.yml-keys",
       status: "warn",
@@ -9321,6 +9333,39 @@ async function checkVaultYmlKeys(vaultRoot) {
     message: "schema ok"
   };
 }
+async function checkClaudeSettings(vaultRoot) {
+  const settingsPath = join2(vaultRoot, ".claude", "settings.json");
+  const file = Bun.file(settingsPath);
+  if (!await file.exists()) {
+    return { check: "claude-settings", status: "ok", message: "no vault settings.json" };
+  }
+  let raw;
+  try {
+    raw = JSON.parse(await file.text());
+  } catch {
+    return {
+      check: "claude-settings",
+      status: "warn",
+      message: "settings.json contains invalid JSON"
+    };
+  }
+  const marketplaces = raw["extraKnownMarketplaces"];
+  const onebrain = marketplaces?.["onebrain"];
+  const source = onebrain?.["source"];
+  const repo = source?.["repo"];
+  if (repo === STALE_MARKETPLACE_REPO) {
+    return {
+      check: "claude-settings",
+      status: "warn",
+      message: "stale marketplace repo",
+      hint: "Run onebrain doctor --fix to rewrite to onebrain-ai/onebrain",
+      details: [
+        `stale extraKnownMarketplaces.onebrain.source.repo: ${STALE_MARKETPLACE_REPO} \u2192 ${CANONICAL_MARKETPLACE_REPO}`
+      ]
+    };
+  }
+  return { check: "claude-settings", status: "ok", message: "ok" };
+}
 function hookPresent(settings, event, cmdSubstring) {
   const groups = settings.hooks?.[event] ?? [];
   return groups.some((g) => g.hooks?.some((h) => (h.command ?? "").includes(cmdSubstring)));
@@ -9407,7 +9452,7 @@ async function checkSettingsHooks(vaultRoot, config) {
     ...okDetails.length > 0 ? { details: okDetails } : {}
   };
 }
-var import_yaml2, STANDARD_FOLDER_KEYS, REQUIRED_PLUGIN_FILES, REQUIRED_PLUGIN_DIRS, STALE_BASH_FILES, REQUIRED_VAULT_YML_KEYS, REQUIRED_FOLDER_KEYS, REQUIRED_HOOKS, ALLOWED_HOOK_EVENTS, QMD_HOOK_SUBSTRING = "onebrain qmd-reindex", ONEBRAIN_COMMAND_SUBSTRING = "onebrain", REQUIRED_PERMISSION = "Bash(onebrain *)", STALE_HOOK_SUBSTRINGS;
+var import_yaml2, STANDARD_FOLDER_KEYS, REQUIRED_PLUGIN_FILES, REQUIRED_PLUGIN_DIRS, STALE_BASH_FILES, REQUIRED_VAULT_YML_KEYS, SOFT_REQUIRED_VAULT_YML_KEYS, REQUIRED_FOLDER_KEYS, STALE_MARKETPLACE_REPO = "kengio/onebrain", CANONICAL_MARKETPLACE_REPO = "onebrain-ai/onebrain", REQUIRED_HOOKS, ALLOWED_HOOK_EVENTS, QMD_HOOK_SUBSTRING = "onebrain qmd-reindex", ONEBRAIN_COMMAND_SUBSTRING = "onebrain", REQUIRED_PERMISSION = "Bash(onebrain *)", STALE_HOOK_SUBSTRINGS;
 var init_validator = __esm(() => {
   import_yaml2 = __toESM(require_dist(), 1);
   STANDARD_FOLDER_KEYS = [
@@ -9431,7 +9476,8 @@ var init_validator = __esm(() => {
     "qmd-reindex.sh",
     "backfill-recapped.sh"
   ];
-  REQUIRED_VAULT_YML_KEYS = ["update_channel", "folders"];
+  REQUIRED_VAULT_YML_KEYS = ["folders"];
+  SOFT_REQUIRED_VAULT_YML_KEYS = ["update_channel"];
   REQUIRED_FOLDER_KEYS = [
     "inbox",
     "projects",
@@ -9449,17 +9495,33 @@ var init_validator = __esm(() => {
   STALE_HOOK_SUBSTRINGS = ["checkpoint-hook.sh", "session-init.sh"];
 });
 
+// src/lib/fs-atomic.ts
+import { rename, unlink, writeFile } from "fs/promises";
+async function atomicWrite(dest, contents, label) {
+  const tmpPath = `${dest}.tmp`;
+  await writeFile(tmpPath, contents, "utf8");
+  try {
+    await rename(tmpPath, dest);
+  } catch (err) {
+    await unlink(tmpPath).catch(() => {});
+    const msg = err instanceof Error ? err.message : String(err);
+    throw new Error(`rename failed for ${label ?? dest}; tmp cleaned up: ${msg}`, { cause: err });
+  }
+}
+var init_fs_atomic = () => {};
+
 // src/lib/index.ts
 var init_lib = __esm(() => {
   init_parser();
   init_validator();
+  init_fs_atomic();
 });
 
 // package.json
 var require_package = __commonJS((exports, module) => {
   module.exports = {
     name: "@onebrain-ai/cli",
-    version: "2.1.9",
+    version: "2.1.11",
     description: "CLI for OneBrain \u2014 personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
     keywords: [
       "onebrain",
@@ -9940,7 +10002,7 @@ __export(exports_register_hooks, {
   runRegisterHooks: () => runRegisterHooks,
   registerHooksCommand: () => registerHooksCommand
 });
-import { mkdir, readFile, rename, writeFile } from "fs/promises";
+import { mkdir, readFile, rename as rename2, writeFile as writeFile2 } from "fs/promises";
 import { homedir } from "os";
 import { dirname, join as join4 } from "path";
 async function readSettings(settingsPath) {
@@ -9956,8 +10018,8 @@ async function readSettings(settingsPath) {
 async function writeSettings(settingsPath, settings) {
   await mkdir(dirname(settingsPath), { recursive: true });
   const tmpPath = `${settingsPath}.tmp`;
-  await writeFile(tmpPath, JSON.stringify(settings, null, 4), "utf8");
-  await rename(tmpPath, settingsPath);
+  await writeFile2(tmpPath, JSON.stringify(settings, null, 4), "utf8");
+  await rename2(tmpPath, settingsPath);
 }
 function checkHookPresence(groups, targetCmd) {
   let foundMigrate = false;
@@ -10086,8 +10148,8 @@ ${ONEBRAIN_MARKER}
 ${PATH_EXPORT}
 `;
   const tmpPath = `${profilePath}.tmp`;
-  await writeFile(tmpPath, updated, "utf8");
-  await rename(tmpPath, profilePath);
+  await writeFile2(tmpPath, updated, "utf8");
+  await rename2(tmpPath, profilePath);
 }
 async function runRegisterHooks(opts = {}) {
   const vaultRoot = opts.vaultDir ?? process.cwd();
@@ -10216,17 +10278,7 @@ __export(exports_vault_sync, {
   vaultSyncCommand: () => vaultSyncCommand,
   runVaultSync: () => runVaultSync
 });
-import {
-  mkdir as mkdir2,
-  mkdtemp,
-  readFile as readFile2,
-  readdir,
-  rename as rename2,
-  rm,
-  stat as stat3,
-  unlink,
-  writeFile as writeFile2
-} from "fs/promises";
+import { mkdir as mkdir2, mkdtemp, readFile as readFile2, readdir, rm, stat as stat3, unlink as unlink2, writeFile as writeFile3 } from "fs/promises";
 import { homedir as homedir2, tmpdir } from "os";
 import { dirname as dirname2, join as join5, relative } from "path";
 function resolveBranch(updateChannel) {
@@ -10250,7 +10302,7 @@ async function downloadTarball(branch, fetchFn) {
 }
 async function extractTarball(tarball, destDir) {
   const tarPath = join5(destDir, "bundle.tar.gz");
-  await writeFile2(tarPath, Buffer.from(tarball));
+  await writeFile3(tarPath, Buffer.from(tarball));
   const proc = Bun.spawn(["tar", "-xzf", tarPath, "-C", destDir], {
     stdout: "pipe",
     stderr: "pipe"
@@ -10260,7 +10312,7 @@ async function extractTarball(tarball, destDir) {
     const errText = await new Response(proc.stderr).text();
     throw new Error(`tar extraction failed (exit ${exitCode}): ${errText.trim()}`);
   }
-  await unlink(tarPath);
+  await unlink2(tarPath);
   const entries = await readdir(destDir);
   const topLevel = entries.find((e2) => e2 !== "bundle.tar.gz");
   if (!topLevel) {
@@ -10296,7 +10348,7 @@ async function listFilesRecursive(dir) {
   }
   return results;
 }
-async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink) {
+async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink2) {
   const sourcePlugin = join5(extractedDir, ".claude", "plugins", "onebrain");
   const destPlugin = join5(vaultRoot, ".claude", "plugins", "onebrain");
   await mkdir2(destPlugin, { recursive: true });
@@ -10316,7 +10368,7 @@ async function syncPluginFiles(extractedDir, vaultRoot, unlinkFn = unlink) {
     const destPath = join5(destPlugin, rel);
     await mkdir2(dirname2(destPath), { recursive: true });
     const content = await readFile2(srcPath);
-    await writeFile2(destPath, content);
+    await writeFile3(destPath, content);
     filesAdded++;
   }
   let filesRemoved = 0;
@@ -10336,7 +10388,7 @@ async function copyRootDocs(extractedDir, vaultRoot) {
     const destPath = join5(vaultRoot, doc);
     try {
       const content = await readFile2(srcPath);
-      await writeFile2(destPath, content);
+      await writeFile3(destPath, content);
     } catch {}
   }
 }
@@ -10353,7 +10405,7 @@ async function mergeHarnessFile(extractedDir, vaultRoot, filename) {
   try {
     vaultText = await readFile2(destPath, "utf8");
   } catch {
-    await writeFile2(destPath, repoText, "utf8");
+    await writeFile3(destPath, repoText, "utf8");
     return repoText.split(`
 `).filter((l2) => l2.startsWith("@")).length;
   }
@@ -10374,7 +10426,7 @@ async function mergeHarnessFile(extractedDir, vaultRoot, filename) {
   }
   const merged = vaultLines.join(`
 `);
-  await writeFile2(destPath, merged, "utf8");
+  await writeFile3(destPath, merged, "utf8");
   return newImports.length;
 }
 async function mergeHarnessFiles(extractedDir, vaultRoot) {
@@ -10396,22 +10448,21 @@ async function updateVaultYml(vaultRoot, updateChannel) {
   }
   const raw = import_yaml3.parse(text) ?? {};
   raw["update_channel"] = updateChannel;
-  const updated = import_yaml3.stringify(raw, { lineWidth: 0 });
-  const tmpPath = `${vaultYmlPath}.tmp`;
-  await writeFile2(tmpPath, updated, "utf8");
-  await rename2(tmpPath, vaultYmlPath);
+  await atomicWrite(vaultYmlPath, import_yaml3.stringify(raw, { lineWidth: 0 }), "vault.yml");
 }
-async function readPluginVersion(vaultRoot) {
+async function readPluginMetadata(vaultRoot) {
   const pluginJsonPath = join5(vaultRoot, ".claude", "plugins", "onebrain", ".claude-plugin", "plugin.json");
   try {
     const text = await readFile2(pluginJsonPath, "utf8");
     const parsed = JSON.parse(text);
-    return typeof parsed["version"] === "string" ? parsed["version"] : "unknown";
+    const version = typeof parsed["version"] === "string" ? parsed["version"] : "unknown";
+    const lastUpdated = typeof parsed["lastUpdated"] === "string" ? parsed["lastUpdated"] : undefined;
+    return { version, lastUpdated };
   } catch {
-    return "unknown";
+    return { version: "unknown", lastUpdated: undefined };
   }
 }
-async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir) {
+async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir, now = () => new Date) {
   let text;
   try {
     text = await readFile2(installedPluginsPath, "utf8");
@@ -10433,7 +10484,8 @@ async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCache
     return { skipped: true };
   }
   const vaultPluginDir = join5(vaultRoot, ".claude", "plugins", "onebrain");
-  const pluginVersion = await readPluginVersion(vaultRoot);
+  const { version: pluginVersion, lastUpdated: pluginLastUpdated } = await readPluginMetadata(vaultRoot);
+  const updatedAt = pluginLastUpdated ?? now().toISOString();
   const cacheDir = installedPluginsCacheDir ?? join5(dirname2(installedPluginsPath), "cache");
   const hasMarketplace = onebrainKeys.some((k2) => {
     const entries = plugins[k2];
@@ -10443,6 +10495,33 @@ async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCache
     return { skipped: true };
   }
   let changed = false;
+  const ONEBRAIN_KEY = "onebrain@onebrain";
+  if (Array.isArray(plugins[ONEBRAIN_KEY])) {
+    const before = plugins[ONEBRAIN_KEY];
+    const keep = [];
+    for (const entry of before) {
+      const projectPath = entry["projectPath"];
+      if (typeof projectPath !== "string") {
+        keep.push(entry);
+        continue;
+      }
+      try {
+        await stat3(projectPath);
+        keep.push(entry);
+      } catch (err) {
+        const code = err?.code;
+        if (code === "ENOENT")
+          continue;
+        process.stderr.write(`vault-sync: pin warning: stat ${projectPath}: ${code ?? "unknown"}
+`);
+        keep.push(entry);
+      }
+    }
+    if (keep.length !== before.length) {
+      plugins[ONEBRAIN_KEY] = keep;
+      changed = true;
+    }
+  }
   for (const key of onebrainKeys) {
     const entries = plugins[key];
     for (const entry of entries) {
@@ -10456,20 +10535,24 @@ async function pinToVault(vaultRoot, installedPluginsPath, installedPluginsCache
       } catch {
         inCache = false;
       }
-      if (!inCache) {
+      const isThisVault = installPath === vaultPluginDir;
+      if (inCache) {
+        entry["installPath"] = vaultPluginDir;
+        changed = true;
+      } else if (!isThisVault) {
         continue;
       }
-      entry["installPath"] = vaultPluginDir;
-      entry["version"] = pluginVersion;
-      changed = true;
+      if (entry["version"] !== pluginVersion) {
+        entry["version"] = pluginVersion;
+        entry["lastUpdated"] = updatedAt;
+        changed = true;
+      }
     }
   }
   if (!changed) {
     return { skipped: false };
   }
-  const tmpPath = `${installedPluginsPath}.tmp`;
-  await writeFile2(tmpPath, JSON.stringify(data, null, 4), "utf8");
-  await rename2(tmpPath, installedPluginsPath);
+  await atomicWrite(installedPluginsPath, JSON.stringify(data, null, 4), "installed_plugins.json");
   return { skipped: false };
 }
 async function cleanPluginCache(installedPluginsPath, installedPluginsCacheDir) {
@@ -10535,7 +10618,7 @@ async function cleanPluginCache(installedPluginsPath, installedPluginsCacheDir)
 async function runVaultSync(vaultRoot, opts = {}) {
   const fetchFn = opts.fetchFn ?? globalThis.fetch;
   const isTTY = opts.isTTY ?? process.stdout.isTTY;
-  const unlinkFn = opts.unlinkFn ?? unlink;
+  const unlinkFn = opts.unlinkFn ?? unlink2;
   let updateChannel = "stable";
   try {
     const vaultYmlText = await readFile2(join5(vaultRoot, "vault.yml"), "utf8");
@@ -10637,7 +10720,7 @@ async function runVaultSync(vaultRoot, opts = {}) {
           const destPath = join5(destObsidian, rel);
           await mkdir2(dirname2(destPath), { recursive: true });
           const content = await readFile2(srcPath);
-          await writeFile2(destPath, content);
+          await writeFile3(destPath, content);
         }
       } catch {}
     }
@@ -10672,7 +10755,7 @@ async function runVaultSync(vaultRoot, opts = {}) {
     if (harness === "claude") {
       startSpinner("\uD83D\uDCCC", "Pinning to vault");
       try {
-        const pinResult = await pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir);
+        const pinResult = await pinToVault(vaultRoot, installedPluginsPath, installedPluginsCacheDir, opts.now);
         result.pinSkipped = pinResult.skipped;
         if (pinResult.skipped) {
           stopSpinner("pin skipped (not found or marketplace)");
@@ -10727,6 +10810,7 @@ async function vaultSyncCommand(vaultRoot, opts = {}) {
 var import_picocolors6, import_yaml3;
 var init_vault_sync = __esm(() => {
   init_dist2();
+  init_lib();
   init_cli_ui();
   init_harness();
   import_picocolors6 = __toESM(require_picocolors(), 1);
@@ -10761,7 +10845,7 @@ var import_picocolors5 = __toESM(require_picocolors(), 1);
 var import_picocolors = __toESM(require_picocolors(), 1);
 function resolveBinaryVersion() {
   if (true)
-    return "2.1.9";
+    return "2.1.11";
   try {
     const pkg = require_package();
     return pkg.version ?? "dev";
@@ -11229,6 +11313,7 @@ async function runDoctor(opts = {}) {
   const checkPluginFilesFn = opts.checkPluginFilesFn ?? checkPluginFiles;
   const checkVaultYmlKeysFn = opts.checkVaultYmlKeysFn ?? checkVaultYmlKeys;
   const checkSettingsHooksFn = opts.checkSettingsHooksFn ?? checkSettingsHooks;
+  const checkClaudeSettingsFn = opts.checkClaudeSettingsFn ?? checkClaudeSettings;
   if (isTTY) {
     await printBanner();
   }
@@ -11259,7 +11344,14 @@ async function runDoctor(opts = {}) {
   if (vaultYmlResult.status === "ok") {
     try {
       config = await loadVaultConfigFn(vaultDir);
-    } catch {}
+    } catch (err) {
+      const code = err?.code;
+      if (code !== "ENOENT") {
+        const msg = err instanceof Error ? err.message : String(err);
+        process.stderr.write(`doctor: vault.yml load warning: ${msg}
+`);
+      }
+    }
   }
   await randDelay();
   sp1?.stop(fmtResult(vaultYmlResult), vaultYmlResult.details);
@@ -11269,6 +11361,7 @@ async function runDoctor(opts = {}) {
   let pluginFilesResult;
   let vaultYmlKeysResult;
   let settingsHooksResult;
+  let claudeSettingsResult;
   if (isTTY) {
     const sp2 = createStep("\u2699\uFE0F", "Config schema");
     vaultYmlKeysResult = await checkVaultYmlKeysFn(vaultDir);
@@ -11294,6 +11387,10 @@ async function runDoctor(opts = {}) {
     qmdResult = await checkQmdEmbeddingsFn(config);
     await randDelay();
     sp7.stop(fmtResult(qmdResult), qmdResult.details);
+    const sp8 = createStep("\uD83D\uDED2", "Marketplace config");
+    claudeSettingsResult = await checkClaudeSettingsFn(vaultDir);
+    await randDelay();
+    sp8.stop(fmtResult(claudeSettingsResult), claudeSettingsResult.details);
   } else {
     [
       foldersResult,
@@ -11301,14 +11398,16 @@ async function runDoctor(opts = {}) {
       orphanResult,
       pluginFilesResult,
       vaultYmlKeysResult,
-      settingsHooksResult
+      settingsHooksResult,
+      claudeSettingsResult
     ] = await Promise.all([
       checkFoldersFn(vaultDir, config),
       checkQmdEmbeddingsFn(config),
       checkOrphanCheckpointsFn(vaultDir, config),
       checkPluginFilesFn(vaultDir),
       checkVaultYmlKeysFn(vaultDir),
-      checkSettingsHooksFn(vaultDir, config)
+      checkSettingsHooksFn(vaultDir, config),
+      checkClaudeSettingsFn(vaultDir)
     ]);
   }
   const results = [
@@ -11318,7 +11417,8 @@ async function runDoctor(opts = {}) {
     pluginFilesResult,
     settingsHooksResult,
     orphanResult,
-    qmdResult
+    qmdResult,
+    claudeSettingsResult
   ];
   const totalChecks = results.length;
   const errorCount = results.filter((r2) => r2.status === "error").length;
@@ -11351,14 +11451,17 @@ async function runDoctor(opts = {}) {
 `);
     }
   }
+  let fixFailedCount = 0;
   if (opts.fix) {
-    await applyFixes(vaultDir, results, isTTY, opts.registerHooksFn);
+    fixFailedCount = await applyFixes(vaultDir, results, isTTY, opts.registerHooksFn);
   }
+  const ok = errorCount === 0 && fixFailedCount === 0;
   return {
-    ok: errorCount === 0,
-    exitCode: errorCount > 0 ? 1 : 0,
+    ok,
+    exitCode: ok ? 0 : 1,
     errorCount,
-    warningCount
+    warningCount,
+    fixFailedCount
   };
 }
 async function doctorCommand(opts = {}) {
@@ -11406,12 +11509,18 @@ function getFix(r2) {
     };
   }
   const hasDeprecatedKeys = r2.details?.some((d) => d.includes("deprecated key: onebrain_version") || d.includes("deprecated key: method") || d.includes("deprecated key: runtime.harness"));
-  if (r2.check === "vault.yml-keys" && r2.status === "warn" && hasDeprecatedKeys) {
+  const hasMissingUpdateChannel = r2.details?.some((d) => d === "missing key: update_channel");
+  if (r2.check === "vault.yml-keys" && r2.status === "warn" && (hasDeprecatedKeys || hasMissingUpdateChannel)) {
     const deprecated = (r2.details ?? []).filter((d) => d.startsWith("deprecated key:")).map((d) => d.slice("deprecated key: ".length).split(" ")[0] ?? d);
-    const description = deprecated.length > 0 ? `Remove deprecated keys from vault.yml: ${deprecated.join(", ")}` : "Remove deprecated keys from vault.yml";
+    const fixParts = [];
+    if (hasMissingUpdateChannel)
+      fixParts.push("add update_channel: stable");
+    if (deprecated.length > 0)
+      fixParts.push(`remove deprecated: ${deprecated.join(", ")}`);
+    const description = fixParts.length > 0 ? `Fix vault.yml: ${fixParts.join("; ")}` : "Fix vault.yml";
     return {
       fn: async (vaultDir) => {
-        const { readFile: readFile2, writeFile: writeFile2, rename: rename2 } = await import("fs/promises");
+        const { readFile: readFile2 } = await import("fs/promises");
         const { join: join5 } = await import("path");
         const { parse: parse3, stringify } = await Promise.resolve().then(() => __toESM(require_dist(), 1));
         const vaultYmlPath = join5(vaultDir, "vault.yml");
@@ -11431,10 +11540,10 @@ function getFix(r2) {
             }
           }
         }
-        const updated = stringify(raw, { lineWidth: 0 });
-        const tmpPath = `${vaultYmlPath}.tmp`;
-        await writeFile2(tmpPath, updated, "utf8");
-        await rename2(tmpPath, vaultYmlPath);
+        if (details.some((d) => d === "missing key: update_channel")) {
+          raw["update_channel"] = "stable";
+        }
+        await atomicWrite(vaultYmlPath, stringify(raw, { lineWidth: 0 }), "vault.yml");
       },
       description
     };
@@ -11469,6 +11578,29 @@ function getFix(r2) {
       description: `Embed ${count} unembedded document(s) (qmd update + embed)`
     };
   }
+  if (r2.check === "claude-settings" && r2.status === "warn" && r2.details?.some((d) => d.startsWith("stale extraKnownMarketplaces.onebrain.source.repo:"))) {
+    return {
+      fn: async (vaultDir) => {
+        const { readFile: readFile2 } = await import("fs/promises");
+        const { join: join5 } = await import("path");
+        const settingsPath = join5(vaultDir, ".claude", "settings.json");
+        const text = await readFile2(settingsPath, "utf8");
+        const raw = JSON.parse(text);
+        const marketplaces = raw["extraKnownMarketplaces"];
+        const onebrain = marketplaces?.["onebrain"];
+        const source = onebrain?.["source"];
+        if (!source || source["repo"] !== "kengio/onebrain")
+          return;
+        source["repo"] = "onebrain-ai/onebrain";
+        const trailingNewline = text.endsWith(`
+`) ? `
+` : "";
+        const updated = `${JSON.stringify(raw, null, 2)}${trailingNewline}`;
+        await atomicWrite(settingsPath, updated, ".claude/settings.json");
+      },
+      description: "Rewrite stale marketplace repo: kengio/onebrain \u2192 onebrain-ai/onebrain"
+    };
+  }
   if (r2.check === "folders" && r2.status === "error" && r2.hint) {
     const missingStr = r2.hint.replace("Missing: ", "");
     return {
@@ -11492,7 +11624,7 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
       writeLine(`${import_picocolors5.default.green("\u25C6")}  Nothing to fix`);
     else
       writeLine("nothing to fix");
-    return;
+    return 0;
   }
   if (isTTY) {
     writeLine("");
@@ -11507,12 +11639,13 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
       barLine(import_picocolors5.default.dim("No"));
       barBlank();
       close(`No changes made \u2014 run ${import_picocolors5.default.cyan("onebrain doctor --fix")} to apply`);
-      return;
+      return 0;
     }
     barLine("Yes");
     barBlank();
   }
   let fixed = 0;
+  let fixFailed = 0;
   const unfixable = [];
   for (const r2 of results) {
     if (r2.status === "ok")
@@ -11528,6 +11661,7 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
       if (isTTY)
         barLine(`${import_picocolors5.default.green("\u25C6")}  ${fix.description}`);
     } catch (err) {
+      fixFailed++;
       const errMsg = err instanceof Error ? err.message : String(err);
       if (isTTY) {
         barLine(`${import_picocolors5.default.yellow("\u25B2")}  Could not fix ${r2.check}: ${errMsg}`);
@@ -11541,6 +11675,9 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
     barBlank();
     if (fixed > 0)
       barLine(`${import_picocolors5.default.green("\u25C6")}  Fixed ${fixed} issue(s)`);
+    if (fixFailed > 0) {
+      barLine(`${import_picocolors5.default.yellow("\u25B2")}  ${fixFailed} fix(es) failed \u2014 see warnings above`);
+    }
     if (unfixable.length > 0) {
       barLine(`${import_picocolors5.default.yellow("\u25B2")}  ${unfixable.length} issue(s) require manual action:`);
       for (const r2 of unfixable) {
@@ -11551,18 +11688,22 @@ async function applyFixes(vaultDir, results, isTTY, registerHooksFn) {
     close("Done");
   } else {
     process.stdout.write(`fixed: ${fixed}
+`);
+    if (fixFailed > 0)
+      process.stdout.write(`fix-failed: ${fixFailed}
 `);
     if (unfixable.length > 0) {
       process.stdout.write(`manual: ${unfixable.map((r2) => r2.check).join(", ")}
 `);
     }
   }
+  return fixFailed;
 }
 
 // src/commands/init.ts
 var import_picocolors7 = __toESM(require_picocolors(), 1);
 var import_yaml4 = __toESM(require_dist(), 1);
-import { mkdir as mkdir3, readFile as readFile3, readdir as readdir2, rename as rename3, stat as stat4, writeFile as writeFile3 } from "fs/promises";
+import { mkdir as mkdir3, readFile as readFile3, readdir as readdir2, rename as rename3, stat as stat4, writeFile as writeFile4 } from "fs/promises";
 import { homedir as homedir3 } from "os";
 import { dirname as dirname3, join as join6 } from "path";
 init_cli_ui();
@@ -11617,7 +11758,7 @@ var VAULT_YML_DEFAULTS = {
 };
 async function writeVaultYml(vaultDir) {
   const content = import_yaml4.stringify(VAULT_YML_DEFAULTS, { lineWidth: 0 });
-  await writeFile3(join6(vaultDir, "vault.yml"), content, "utf8");
+  await writeFile4(join6(vaultDir, "vault.yml"), content, "utf8");
 }
 async function downloadPluginFiles(vaultDir, vaultSyncFn) {
   const pluginJsonPath = join6(vaultDir, ".claude", "plugins", "onebrain", ".claude-plugin", "plugin.json");
@@ -11706,7 +11847,7 @@ async function registerPlugin(vaultDir, installedPluginsPath) {
   const tmpPath = `${installedPluginsPath}.tmp`;
   try {
     await mkdir3(dirname3(installedPluginsPath), { recursive: true });
-    await writeFile3(tmpPath, JSON.stringify(data, null, 4), "utf8");
+    await writeFile4(tmpPath, JSON.stringify(data, null, 4), "utf8");
     await rename3(tmpPath, installedPluginsPath);
   } catch (err) {
     const msg = err instanceof Error ? err.message : String(err);
@@ -11817,7 +11958,7 @@ async function installObsidianPlugins(vaultDir, opts) {
           throw new Error(`HTTP ${resp.status}`);
         }
         const buf = await resp.arrayBuffer();
-        await writeFile3(join6(pluginDir, assetName), Buffer.from(buf));
+        await writeFile4(join6(pluginDir, assetName), Buffer.from(buf));
       } catch (err) {
         if (assetName === "styles.css")
           continue;
@@ -12201,7 +12342,7 @@ async function checkpointCommand(mode, token, vaultRoot) {
 // src/commands/internal/migrate.ts
 init_lib();
 var import_yaml5 = __toESM(require_dist(), 1);
-import { readFile as readFile4, readdir as readdir3, writeFile as writeFile4 } from "fs/promises";
+import { readFile as readFile4, readdir as readdir3, writeFile as writeFile5 } from "fs/promises";
 import { join as join8 } from "path";
 function parseFrontmatterWithRest(rawText) {
   const text = rawText.replace(/\r\n/g, `
@@ -12258,7 +12399,7 @@ async function runBackfillRecapped(logsFolder, cutoffDate) {
       const files = await listMdFiles(monthPath);
       for (const fname of files) {
         const fpath = join8(monthPath, fname);
-        if (fname.includes("-checkpoint-")) {
+        if (!fname.includes("-session-")) {
           continue;
         }
         if (cutoffDate) {
@@ -12285,7 +12426,7 @@ async function runBackfillRecapped(logsFolder, cutoffDate) {
           const updatedContent = `---
 ${updatedFm}---
 ${rest}`;
-          await writeFile4(fpath, updatedContent, "utf8");
+          await writeFile5(fpath, updatedContent, "utf8");
           backfilled++;
         } catch (error) {
           process.stderr.write(`migrate: error processing ${fname}: ${error}
@@ -12355,7 +12496,7 @@ async function listMdFiles2(dir) {
 }
 async function hasManualSessionLog(monthDir, date) {
   const files = await listMdFiles2(monthDir);
-  const sessionLogs = files.filter((f2) => f2.startsWith(date) && !f2.includes("-checkpoint-") && f2.endsWith(".md"));
+  const sessionLogs = files.filter((f2) => f2.startsWith(date) && f2.includes("-session-") && f2.endsWith(".md"));
   for (const logName of sessionLogs) {
     try {
       const content = await readFile5(join9(monthDir, logName), "utf8");
@@ -12451,7 +12592,7 @@ init_register_hooks();
 
 // src/commands/internal/session-init.ts
 init_lib();
-import { unlink as unlink2 } from "fs/promises";
+import { unlink as unlink3 } from "fs/promises";
 import { tmpdir as osTmpdir2 } from "os";
 import { join as join10 } from "path";
 var DAY_NAMES = ["Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"];
@@ -12564,7 +12705,7 @@ async function cleanStaleStateFile(token, tmpDir) {
     const mtimeMs = mtime instanceof Date ? mtime.getTime() : Number(mtime) * 1000;
     if (mtimeMs < processStartMs) {
       try {
-        await unlink2(stateFile);
+        await unlink3(stateFile);
       } catch {}
     }
   } catch {}
@@ -12848,8 +12989,8 @@ function patchUtf8(stream) {
 }
 
 // src/index.ts
-var VERSION = "2.1.9";
-var RELEASE_DATE = "2026-05-05";
+var VERSION = "2.1.11";
+var RELEASE_DATE = "2026-05-06";
 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": "2.1.9",
+  "version": "2.1.11",
   "description": "CLI for OneBrain — personal AI OS for Obsidian with persistent memory, 24+ skills, and Claude Code integration",
   "keywords": [
     "onebrain",