@bohuyeshan/openagent-labforge-core 3.11.5 → 3.13.0

package/README.md

@@ -1,584 +1,229 @@
-> [!WARNING]
-> **TEMP NOTICE (This Week): Reduced Maintainer Availability**
->
-> Core maintainer Q got injured, so issue/PR responses and releases may be delayed this week.
-> Thank you for your patience and support.
-
-> [!NOTE]
-> **Derivative Notice**
-> 
-> This project is a fork/derivative of `code-yeongyu/openagent-labforge` (formerly `openagent-labforge`).
-> We have renamed the project and added new features and configuration options focused on user-controlled model routing and research workflows.
-> Licensing and provenance are documented in `LICENSE.md`, `NOTICE`, `THIRD_PARTY_NOTICES.md`, and `docs/licensing.md`.
->
-> [![Sisyphus Labs - Sisyphus is the agent that codes like your team.](./.github/assets/sisyphuslabs.png?v=2)](https://sisyphuslabs.ai)
-> > **We're building a fully productized version of Sisyphus to define the future of frontier agents. <br />Join the waitlist [here](https://sisyphuslabs.ai).**
-
-> [!TIP]
-> Be with us!
->
-> | [<img alt="Discord link" src="https://img.shields.io/discord/1452487457085063218?color=5865F2&label=discord&labelColor=black&logo=discord&logoColor=white&style=flat-square" width="156px" />](https://discord.gg/PUwSMR9XNk) | Join our [Discord community](https://discord.gg/PUwSMR9XNk) to connect with contributors and fellow `openagent-labforge` users. |
-> | :-----| :----- |
-> | [<img alt="X link" src="https://img.shields.io/badge/Follow-%40justsisyphus-00CED1?style=flat-square&logo=x&labelColor=black" width="156px" />](https://x.com/justsisyphus) | News and updates for `openagent-labforge` used to be posted on my X account. <br /> Since it was suspended mistakenly, [@justsisyphus](https://x.com/justsisyphus) now posts updates on my behalf. |
-> | [<img alt="GitHub Follow" src="https://img.shields.io/github/followers/code-yeongyu?style=flat-square&logo=github&labelColor=black&color=24292f" width="156px" />](https://github.com/code-yeongyu) | Follow [@code-yeongyu](https://github.com/code-yeongyu) on GitHub for more projects. |
-
-<!-- <CENTERED SECTION FOR GITHUB DISPLAY> -->
-
-<div align="center">
-
-[![OpenAgent Labforge](./.github/assets/hero.jpg)](https://github.com/code-yeongyu/openagent-labforge#openagent-labforge)
-
-[![Preview](./.github/assets/omo.png)](https://github.com/code-yeongyu/openagent-labforge#openagent-labforge)
-
-
-</div>
-
-> Anthropic [**blocked OpenCode because of us.**](https://x.com/thdxr/status/2010149530486911014) **Yes this is true.**
-> They want you locked in. Claude Code's a nice prison, but it's still a prison.
->
-> We don't do lock-in here. We ride every model. Claude / Kimi / GLM for orchestration. GPT for reasoning. Minimax for speed. Gemini for creativity.
-> The future isn't picking one winner—it's orchestrating them all. Models get cheaper every month. Smarter every month. No single provider will dominate. We're building for that open market, not their walled gardens.
-
-<div align="center">
-
-[![GitHub Release](https://img.shields.io/github/v/release/code-yeongyu/openagent-labforge?color=369eff&labelColor=black&logo=github&style=flat-square)](https://github.com/code-yeongyu/openagent-labforge/releases)
-[![npm downloads](https://img.shields.io/endpoint?url=https%3A%2F%2Fohmyopenagent.com%2Fapi%2Fnpm-downloads&style=flat-square)](https://www.npmjs.com/package/openagent-labforge)
-[![GitHub Contributors](https://img.shields.io/github/contributors/code-yeongyu/openagent-labforge?color=c4f042&labelColor=black&style=flat-square)](https://github.com/code-yeongyu/openagent-labforge/graphs/contributors)
-[![GitHub Forks](https://img.shields.io/github/forks/code-yeongyu/openagent-labforge?color=8ae8ff&labelColor=black&style=flat-square)](https://github.com/code-yeongyu/openagent-labforge/network/members)
-[![GitHub Stars](https://img.shields.io/github/stars/code-yeongyu/openagent-labforge?color=ffcb47&labelColor=black&style=flat-square)](https://github.com/code-yeongyu/openagent-labforge/stargazers)
-[![GitHub Issues](https://img.shields.io/github/issues/code-yeongyu/openagent-labforge?color=ff80eb&labelColor=black&style=flat-square)](https://github.com/code-yeongyu/openagent-labforge/issues)
-[![License](https://img.shields.io/badge/license-SUL--1.0-white?labelColor=black&style=flat-square)](https://github.com/code-yeongyu/openagent-labforge/blob/dev/LICENSE.md)
-[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/code-yeongyu/openagent-labforge)
-
-[English](README.md) | [한국어](README.ko.md) | [日本語](README.ja.md) | [简体中文](README.zh-cn.md)
-
-</div>
-
-<!-- </CENTERED SECTION FOR GITHUB DISPLAY> -->
-
-## Reviews
-
-> "It made me cancel my Cursor subscription. Unbelievable things are happening in the open source community." - [Arthur Guiot](https://x.com/arthur_guiot/status/2008736347092382053?s=20)
-
-> "If Claude Code does in 7 days what a human does in 3 months, Sisyphus does it in 1 hour. It just works until the task is done. It is a discipline agent." <br/>- B, Quant Researcher
-
-> "Knocked out 8000 eslint warnings with OpenAgent Labforge, just in a day" <br/>- [Jacob Ferrari](https://x.com/jacobferrari_/status/2003258761952289061)
-
-> "I converted a 45k line tauri app into a SaaS web app overnight using Ohmyopencode and ralph loop. Started with interview me prompt, asked it for ratings and recommendations on the questions. It was amazing to watch it work and to wake up this morning to a mostly working website!" - [James Hargis](https://x.com/hargabyte/status/2007299688261882202)
-
-> "use openagent-labforge, you will never go back" <br/>- [d0t3ch](https://x.com/d0t3ch/status/2001685618200580503)
-
-> "I haven't really been able to articulate exactly what makes it so great yet, but the development experience has reached a completely different dimension." - [
-苔硯:こけすずり](https://x.com/kokesuzuri/status/2008532913961529372?s=20)
-
-> "Experimenting with open code, OpenAgent Labforge and supermemory this weekend to build some minecraft/souls-like abomination."
-> "Asking it to add crouch animations while I go take my post-lunch walk. [Video]" - [MagiMetal](https://x.com/MagiMetal/status/2005374704178373023)
-
-> "You guys should pull this into core and recruit him. Seriously. It's really, really, really good." <br/>- Henning Kilset
-
-> "Hire @yeon_gyu_kim if you can convince him, this dude has revolutionized opencode." <br/>- [mysticaltech](https://x.com/mysticaltech/status/2001858758608376079)
-
-> "OpenAgent Labforge Is Actually Insane" - [YouTube - Darren Builds AI](https://www.youtube.com/watch?v=G_Snfh2M41M)
-
----
-
-# OpenAgent Labforge
-
-You're juggling Claude Code, Codex, random OSS models. Configuring workflows. Debugging agents.
-
-We did the work. Tested everything. Kept what actually shipped.
-
-Install OmO. Type `ultrawork`. Done.
-
-## Change Summary (Labforge)
-
-- Renamed fork with a derivative notice and third-party provenance.
-- Restored lightweight default plan and build behavior with explicit toggles.
-- Added Model Governor AUTO for discovery, category defaults, and fallback chains.
-- Enforced manual model selection priority to prevent unwanted overrides.
-- Added i18n agent display names and SOUL rule injection controls.
-- Added built-in skills for DOCX, PDF, PPTX, XLSX, web research, and data analysis.
-- Added research-oriented MCP defaults, explicit MCP policy, and visible default-off research MCPs.
-- Added unified `full` / `paper` skills bundles with source-aware naming and bundle loading.
-- Reduced skill initialization overhead with metadata-first preview and lazy merged-skill access.
-- Hardened todo continuation behavior to better respect user-facing question/confirmation flows.
-
-## Research-Focused Design
-
-- This derivative keeps the original programming strengths and adds research-oriented defaults directly in core.
-- Core now includes model governance, SOUL injection controls, and document/research skill presets.
-- Skills now support a unified functional catalog with metadata-first preview and lazy body loading.
-- Curated skills are split into `paper` and `full` bundles for lower token overhead at runtime.
-- Companion plugins are still recommended for domain depth:
-  - `opencode-agent-bio-paper`
-  - `opencode-mcp-paper-search`
-- See `plugins/BUNDLES.md` for `full` and `paper-only` bundle profiles.
-
-## Unified Skills Catalog
-
-- Generate the curated functional catalog:
-
-```bash
-bun run build:skills-catalog
-```
-
-- Use the runtime bundle shortcut:
-
-```jsonc
-{
-  "skills": {
-    "bundle": "full"
-  }
-}
-```
-
-or:
-
-```jsonc
-{
-  "skills": {
-    "bundle": "paper"
-  }
-}
-```
-
-- Generated outputs:
-  - `generated/skills-bundles/catalog.json`
-  - `generated/skills-bundles/full/INDEX.md`
-  - `generated/skills-bundles/paper/INDEX.md`
-
-The model now previews skill `name`, `description`, and `category` first, then reads full skill instructions only when needed.
-
-To avoid collisions between curated sources, external bundle skills use source-prefixed IDs (for example `openai-curated/openai-docs`, `anthropic/mcp-builder`), while builtin skills keep their original stable names.
-
-## Model Selection Guarantee
-
-- User-selected model is treated as highest priority across build/plan and all added agents.
-- AUTO is explicit (`auto` provider entry) and does not override explicit model pinning.
-- Strict lock is enabled by default and configurable:
-
-```jsonc
-{
-  "experimental": {
-    "strict_user_model_priority": true
-  }
-}
-```
-
-
-## Installation
-
-### Published Package
-
-- Core package: `@bohuyeshan/openagent-labforge-core`
-- Current published version line: `3.11.x`
-- Legacy `@labforge/...` references remain in some historical docs and migration notes only
-
-## Current Distribution Policy
-
-- Current recommended usage: **npm install from the published package**
-- Local build + local install remains available for development and debugging
-- Upstream publish workflow differences are tracked in `docs/release/upstream-publish-notes.md`
-
-## Recommended Current Usage
-
-1. Install from npm:
-
-```bash
-npm install --prefix ~/.config/opencode @bohuyeshan/openagent-labforge-core@latest
-```
-
-2. Register the plugin in `opencode.json`:
-
-```jsonc
-{
-  "plugin": ["@bohuyeshan/openagent-labforge-core"]
-}
-```
-
-3. Use the bundle shortcut in plugin config:
-
-```bash
-bun run build:skills-catalog
-bun run build
-```
-
-```jsonc
-{
-  "skills": {
-    "bundle": "full"
-  }
-}
-```
-
-4. Use `paper` if you want a smaller research-focused runtime surface.
-
-5. Local development path (optional):
-
-```bash
-bun run build:skills-catalog
-bun run build
-npm pack
-npm install --prefix ~/.config/opencode /absolute/path/to/openagent-labforge-core-<version>.tgz
-```
-
-## Current Runtime Behavior
-
-- User-selected model remains highest priority across sessions and agents.
-- OpenAI-compatible providers such as `gmn` should keep a single GPT model entry (for example `gmn/gpt-5.3-codex`) and let the OpenCode UI control reasoning depth.
-- `skills.bundle = "full"` currently loads the complete curated bundle (builtin + curated external skills).
-- External bundle skills use source-prefixed IDs (for example `openai-curated/openai-docs`) to avoid collision with builtin skills.
-- Todo continuation is now more conservative:
-  - waits for a second idle cycle before injecting continuation
-  - respects `question` tool usage and common textual “waiting for user” patterns
-  - avoids immediate repeated continuation reinjection
-
-## Current Known Limits
-
-- Multi-window / multi-repository switching still depends partly on OpenCode host-side initialization behavior.
-- The plugin now avoids several repeated scans, but `createSkillContext` and host-side session loading can still add noticeable cold-start cost in very large workspaces or long-running OpenCode installations.
-- Large OpenCode host storage, stale session state, and very large workspaces can still make session hydration feel slower than raw startup.
-
-## Provider Note
-
-For OpenAI-compatible providers such as `gmn`, prefer a config shape like:
-
-```jsonc
-{
-  "provider": {
-    "gmn": {
-      "npm": "@ai-sdk/openai",
-      "options": {
-        "baseURL": "https://gmn.chuangzuoli.com/v1"
-      },
-      "models": {
-        "gpt-5.3-codex": {
-          "name": "GPT-5.3 Codex",
-          "limit": {
-            "context": 400000,
-            "output": 128000
-          }
-        }
-      }
-    }
-  },
-  "model": "gmn/gpt-5.3-codex"
-}
-```
-
-Keep reasoning depth in the OpenCode UI instead of hardcoding separate `low` / `medium` / `high` model aliases.
-
-### For Humans
-
-Copy and paste this prompt to your LLM agent (Claude Code, AmpCode, Cursor, etc.):
-
-```
-Install and configure @bohuyeshan/openagent-labforge-core by following the instructions here:
-https://raw.githubusercontent.com/code-yeongyu/openagent-labforge/refs/heads/dev/docs/guide/installation.md
-```
-
-Or read the [Installation Guide](docs/guide/installation.md), but seriously, let an agent do it. Humans fat-finger configs.
-
-### For LLM Agents
-
-Fetch the installation guide and follow it:
-
-```bash
-curl -s https://raw.githubusercontent.com/code-yeongyu/openagent-labforge/refs/heads/dev/docs/guide/installation.md
-```
-
----
-
-## Skip This README
-
-We're past the era of reading docs. Just paste this into your agent:
-
-```
-Read this and tell me why it's not just another boilerplate: https://raw.githubusercontent.com/code-yeongyu/openagent-labforge/refs/heads/dev/README.md
-```
-
-## Highlights
-
-### 🪄 `ultrawork`
-
-You're actually reading this? Wild.
-
-Install. Type `ultrawork` (or `ulw`). Done.
-
-Everything below, every feature, every optimization, you don't need to know it. It just works.
-
-Even only with following subscriptions, ultrawork will work well (this project is not affiliated, this is just personal recommendation):
-- [ChatGPT Subscription ($20)](https://chatgpt.com/)
-- [Kimi Code Subscription ($0.99) (*only this month)](https://www.kimi.com/kimiplus/sale)
-- [GLM Coding Plan ($10)](https://z.ai/subscribe)
-- If you are eligible for pay-per-token, using kimi and gemini models won't cost you that much.
-
-|       | Feature                                                  | What it does                                                                                                                                                                                                     |
-| :---: | :------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-|   🤖   | **Discipline Agents**                                    | Sisyphus orchestrates Hephaestus, Oracle, Librarian, Explore. A full AI dev team in parallel.                                                                                                                    |
-|   ⚡   | **`ultrawork` / `ulw`**                                  | One word. Every agent activates. Doesn't stop until done.                                                                                                                                                        |
-|   🚪   | **[IntentGate](https://factory.ai/news/terminal-bench)** | Analyzes true user intent before classifying or acting. No more literal misinterpretations.                                                                                                                      |
-|   🔗   | **Hash-Anchored Edit Tool**                              | `LINE#ID` content hash validates every change. Zero stale-line errors. Inspired by [oh-my-pi](https://github.com/can1357/oh-my-pi). [The Harness Problem →](https://blog.can.ac/2026/02/12/the-harness-problem/) |
-|   🛠️   | **LSP + AST-Grep**                                       | Workspace rename, pre-build diagnostics, AST-aware rewrites. IDE precision for agents.                                                                                                                           |
-|   🧠   | **Background Agents**                                    | Fire 5+ specialists in parallel. Context stays lean. Results when ready.                                                                                                                                         |
-|   📚   | **Built-in MCPs**                                        | Exa (web search), Context7 (official docs), Grep.app (GitHub search). Always on.                                                                                                                                 |
-|   🔁   | **Ralph Loop / `/ulw-loop`**                             | Self-referential loop. Doesn't stop until 100% done.                                                                                                                                                             |
-|   ✅   | **Todo Enforcer**                                        | Agent goes idle? System yanks it back. Your task gets done, period.                                                                                                                                              |
-|   💬   | **Comment Checker**                                      | No AI slop in comments. Code reads like a senior wrote it.                                                                                                                                                       |
-|   🖥️   | **Tmux Integration**                                     | Full interactive terminal. REPLs, debuggers, TUIs. All live.                                                                                                                                                     |
-|   🔌   | **Claude Code Compatible**                               | Your hooks, commands, skills, MCPs, and plugins? All work here.                                                                                                                                                  |
-|   🎯   | **Skill-Embedded MCPs**                                  | Skills carry their own MCP servers. No context bloat.                                                                                                                                                            |
-|   📋   | **Prometheus Planner**                                   | Interview-mode strategic planning before any execution.                                                                                                                                                          |
-|   🔍   | **`/init-deep`**                                         | Auto-generates hierarchical `AGENTS.md` files throughout your project. Great for both token efficiency and your agent's performance                                                                              |
-
-### Discipline Agents
-
-<table><tr>
-<td align="center"><img src=".github/assets/sisyphus.png" height="300" /></td>
-<td align="center"><img src=".github/assets/hephaestus.png" height="300" /></td>
-</tr></table>
-
-**Sisyphus** (`claude-opus-4-6` / **`kimi-k2.5`** / **`glm-5`** ) is your main orchestrator. He plans, delegates to specialists, and drives tasks to completion with aggressive parallel execution. He does not stop halfway.
-
-**Hephaestus** (`gpt-5.3-codex`) is your autonomous deep worker. Give him a goal, not a recipe. He explores the codebase, researches patterns, and executes end-to-end without hand-holding. *The Legitimate Craftsman.*
-
-**Prometheus** (`claude-opus-4-6` / **`kimi-k2.5`** / **`glm-5`** ) is your strategic planner. Interview mode: it questions, identifies scope, and builds a detailed plan before a single line of code is touched.
-
-Every agent is tuned to its model's specific strengths. No manual model-juggling. [Learn more →](docs/guide/overview.md)
-
-> Anthropic [blocked OpenCode because of us.](https://x.com/thdxr/status/2010149530486911014) That's why Hephaestus is called "The Legitimate Craftsman." The irony is intentional.
->
-> We run best on Opus, but Kimi K2.5 + GPT-5.3 Codex already beats vanilla Claude Code. Zero config needed.
-
-### Agent Orchestration
-
-When Sisyphus delegates to a subagent, it doesn't pick a model. It picks a **category**. The category maps automatically to the right model:
-
-| Category             | What it's for                      |
-| :------------------- | :--------------------------------- |
-| `visual-engineering` | Frontend, UI/UX, design            |
-| `deep`               | Autonomous research + execution    |
-| `quick`              | Single-file changes, typos         |
-| `ultrabrain`         | Hard logic, architecture decisions |
-
-Agent says what kind of work. Harness picks the right model. `ultrabrain` now routes to GPT-5.4 xhigh by default. You touch nothing.
-
-### Model Governor (AUTO)
-
-AUTO detects available models, assigns category defaults, and builds fallback chains.
-It never overwrites your explicit config or UI-selected model.
-
-Config example:
-
-```jsonc
-{
-  "model_governor": {
-    "enabled": true,
-    "mode": "auto",
-    "report": { "enabled": true, "format": "md" }
-  }
-}
-```
-
-Reports and rules are written to your OpenCode config dir:
-
-- `openagent-labforge.models.report.md`
-- `openagent-labforge.models.rules.jsonc`
-
-### Claude Code Compatibility
-
-You dialed in your Claude Code setup. Good.
-
-Every hook, command, skill, MCP, plugin works here unchanged. Full compatibility, including plugins.
-
-### World-Class Tools for Your Agents
-
-LSP, AST-Grep, Tmux, MCP actually integrated, not duct-taped together.
-
-- **LSP**: `lsp_rename`, `lsp_goto_definition`, `lsp_find_references`, `lsp_diagnostics`. IDE precision for every agent
-- **AST-Grep**: Pattern-aware code search and rewriting across 25 languages
-- **Tmux**: Full interactive terminal. REPLs, debuggers, TUI apps. Your agent stays in session
-- **MCP**: Web search, official docs, GitHub code search. All baked in
-
-### Skill-Embedded MCPs
-
-MCP servers eat your context budget. We fixed that.
-
-Skills bring their own MCP servers. Spin up on-demand, scoped to task, gone when done. Context window stays clean.
-
-### Codes Better. Hash-Anchored Edits
-
-The harness problem is real. Most agent failures aren't the model. It's the edit tool.
-
-> *"None of these tools give the model a stable, verifiable identifier for the lines it wants to change... They all rely on the model reproducing content it already saw. When it can't - and it often can't - the user blames the model."*
->
-> <br/>- [Can Bölük, The Harness Problem](https://blog.can.ac/2026/02/12/the-harness-problem/)
-
-Inspired by [oh-my-pi](https://github.com/can1357/oh-my-pi), we implemented **Hashline**. Every line the agent reads comes back tagged with a content hash:
-
-```
-11#VK| function hello() {
-22#XJ|   return "world";
-33#MB| }
-```
-
-The agent edits by referencing those tags. If the file changed since the last read, the hash won't match and the edit is rejected before corruption. No whitespace reproduction. No stale-line errors.
-
-Grok Code Fast 1: **6.7% → 68.3%** success rate. Just from changing the edit tool.
-
-### Deep Initialization. `/init-deep`
-
-Run `/init-deep`. It generates hierarchical `AGENTS.md` files:
-
-```
-project/
-├── AGENTS.md              ← project-wide context
-├── src/
-│   ├── AGENTS.md          ← src-specific context
-│   └── components/
-│       └── AGENTS.md      ← component-specific context
-```
-
-Agents auto-read relevant context. Zero manual management.
-
-### Planning. Prometheus
-
-Complex task? Don't prompt and pray.
-
-`/start-work` calls Prometheus. **Interviews you like a real engineer**, identifies scope and ambiguities, builds a verified plan before touching code. Agent knows what it's building before it starts.
-
-### Skills
-
-Skills aren't just prompts. Each brings:
-
-- Domain-tuned system instructions
-- Embedded MCP servers, on-demand
-- Scoped permissions. Agents stay in bounds
-
-Built-ins: `playwright` (browser automation), `git-master` (atomic commits, rebase surgery), `frontend-ui-ux` (design-first UI).
-
-Add your own: `.opencode/skills/*/SKILL.md` or `~/.config/opencode/skills/*/SKILL.md`.
-
-**Want the full feature breakdown?** See the **[Features Documentation](docs/reference/features.md)** for agents, hooks, tools, MCPs, and everything else in detail.
-
----
-
-> **New to openagent-labforge?** Read the **[Overview](docs/guide/overview.md)** to understand what you have, or check the **[Orchestration Guide](docs/guide/orchestration.md)** for how agents collaborate.
-
-## Uninstallation
-
-To remove openagent-labforge:
-
-1. **Remove the plugin from your OpenCode config**
-
-   Edit `~/.config/opencode/opencode.json` (or `opencode.jsonc`) and remove `"openagent-labforge"` from the `plugin` array:
-
-   ```bash
-   # Using jq
-   jq '.plugin = [.plugin[] | select(. != "openagent-labforge")]' \
-       ~/.config/opencode/opencode.json > /tmp/oc.json && \
-       mv /tmp/oc.json ~/.config/opencode/opencode.json
-   ```
-
-2. **Remove configuration files (optional)**
-
-   ```bash
-   # Remove user config
-   rm -f ~/.config/opencode/openagent-labforge.json ~/.config/opencode/openagent-labforge.jsonc
-
-   # Remove project config (if exists)
-   rm -f .opencode/openagent-labforge.json .opencode/openagent-labforge.jsonc
-   ```
-
-3. **Verify removal**
-
-   ```bash
-   opencode --version
-   # Plugin should no longer be loaded
-   ```
-
-## Features
-
-Features you'll think should've always existed. Once you use them, you can't go back.
-
-See full [Features Documentation](docs/reference/features.md).
-
-**Quick Overview:**
-- **Agents**: Sisyphus (the main agent), Prometheus (planner), Oracle (architecture/debugging), Librarian (docs/code search), Explore (fast codebase grep), Multimodal Looker
-- **Background Agents**: Run multiple agents in parallel like a real dev team
-- **LSP & AST Tools**: Refactoring, rename, diagnostics, AST-aware code search
-- **Hash-anchored Edit Tool**: `LINE#ID` references validate content before applying every change. Surgical edits, zero stale-line errors
-- **Context Injection**: Auto-inject AGENTS.md, README.md, conditional rules
-- **Claude Code Compatibility**: Full hook system, commands, skills, agents, MCPs
-- **Built-in MCPs**: websearch (Exa), context7 (docs), grep_app (GitHub search)
-- **Session Tools**: List, read, search, and analyze session history
-- **Productivity Features**: Ralph Loop, Todo Enforcer, GPT permission-tail continuation, Comment Checker, Think Mode, and more
-- **Model Setup**: Agent-model matching is built into the [Installation Guide](docs/guide/installation.md#step-5-understand-your-model-setup)
-
-## Configuration
-
-Opinionated defaults, adjustable if you insist.
-
-See [Configuration Documentation](docs/reference/configuration.md).
-
-**Quick Overview:**
-- **Config Locations**: `.opencode/openagent-labforge.jsonc` or `.opencode/openagent-labforge.json` (project), `~/.config/opencode/openagent-labforge.jsonc` or `~/.config/opencode/openagent-labforge.json` (user)
-- **JSONC Support**: Comments and trailing commas supported
-- **Agents**: Override models, temperatures, prompts, and permissions for any agent
-- **Built-in Skills**: `playwright` (browser automation), `git-master` (atomic commits)
-- **Sisyphus Agent**: Main orchestrator with Prometheus (Planner) and Metis (Plan Consultant)
-- **Background Tasks**: Configure concurrency limits per provider/model
-- **Categories**: Domain-specific task delegation (`visual`, `business-logic`, custom)
-- **Hooks**: 25+ built-in hooks, including `gpt-permission-continuation`, all configurable via `disabled_hooks`
-- **MCPs**: Built-in websearch (Exa), context7 (docs), grep_app (GitHub search)
-- **LSP**: Full LSP support with refactoring tools
-- **Experimental**: Aggressive truncation, auto-resume, and more
-
-
-## Author's Note
-
-**Want the philosophy?** Read the [Ultrawork Manifesto](docs/manifesto.md).
-
----
-
-I burned through $24K in LLM tokens on personal projects. Tried every tool. Configured everything to death. OpenCode won.
-
-Every problem I hit, the fix is baked into this plugin. Install and go.
-
-If OpenCode is Debian/Arch, OmO is Ubuntu/[Omarchy](https://omarchy.org/).
-
-Heavy influence from [AmpCode](https://ampcode.com) and [Claude Code](https://code.claude.com/docs/overview). Features ported, often improved. Still building. It's **Open**Code.
-
-Other harnesses promise multi-model orchestration. We ship it. Stability too. And features that actually work.
-
-I'm this project's most obsessive user:
-- Which model has the sharpest logic?
-- Who's the debugging god?
-- Who writes the best prose?
-- Who dominates frontend?
-- Who owns backend?
-- What's fastest for daily driving?
-- What are competitors shipping?
-
-This plugin is the distillation. Take the best. Got improvements? PRs welcome.
-
-**Stop agonizing over harness choices.**
-**I'll research, steal the best, and ship it here.**
-
-Sounds arrogant? Have a better way? Contribute. You're welcome.
-
-No affiliation with any project/model mentioned. Just personal experimentation.
-
-99% of this project was built with OpenCode. I don't really know TypeScript. **But I personally reviewed and largely rewrote this doc.**
-
-## Loved by professionals at
-
-- [Indent](https://indentcorp.com)
-  - Making Spray - influencer marketing solution, vovushop - crossborder commerce platform, vreview - ai commerce review marketing solution
-- [Google](https://google.com)
-- [Microsoft](https://microsoft.com)
-- [ELESTYLE](https://elestyle.jp)
-  - Making elepay - multi-mobile payment gateway, OneQR - mobile application SaaS for cashless solutions
-
-*Special thanks to [@junhoyeo](https://github.com/junhoyeo) for this amazing hero image.*
-
+# OpenAgent Labforge
+
+OpenAgent Labforge is an OpenCode plugin fork focused on three things:
+
+- stronger engineering-oriented orchestration
+- explicit, inspectable child-session delegation
+- bioinformatics-first specialist workflows
+
+It is a derivative of `code-yeongyu/oh-my-openagent` and keeps upstream
+license/provenance boundaries intact. See [LICENSE.md](LICENSE.md),
+[NOTICE](NOTICE), [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md), and
+[docs/licensing.md](docs/licensing.md).
+
+## What This Fork Is Now
+
+This README describes current runtime behavior only.
+
+The plugin is now centered on:
+
+- OpenCode-native delegation through `task(subagent_type=...)`
+- stable plugin/agent/MCP injection for newer OpenCode behavior
+- explicit search/doc/code/paper retrieval separation
+- a growing first-party bioinformatics agent and skill stack
+- local-first development and installation
+
+## Current Core Capabilities
+
+### Engineering orchestration
+
+- `sisyphus`: main orchestrator
+- `wase`: fully autonomous orchestrator
+- `hephaestus`: deep coding executor
+- `prometheus`: planner
+- `atlas`: execution coordinator
+- `metis`: pre-planning consultant
+- `momus`: plan reviewer
+
+These core agents are being upgraded with stronger engineering behavior:
+
+- better scope discipline
+- stronger verification expectations
+- more explicit planning and review standards
+- cleaner delegation contracts
+
+Current engineering-capability layering:
+
+- strong execution + orchestration: `sisyphus`, `wase`
+- strong execution: `hephaestus`
+- strong orchestration: `atlas`
+- strong planning: `prometheus`, `metis`
+- strong review: `momus`
+
+This layering is intentional so future de-duplication stays easy if OpenCode
+itself absorbs parts of the same capability set.
+
+### Specialist agents
+
+- `explore`: local codebase discovery
+- `librarian`: focused upstream docs / SDK / library research
+- `github-scout`: repository and implementation scouting
+- `tech-scout`: ecosystem / benchmark / launch analysis
+- `article-writer`: public technical writing
+- `scientific-writer`: research-facing technical writing
+- `multimodal-looker`: PDF / image / figure understanding
+
+### Bioinformatics stack
+
+The fork now has an explicit bioinformatics hierarchy:
+
+- main bio entrypoints:
+  `bio-orchestrator` for integrated coordination
+  `bio-pipeline-operator` for execution-focused work
+- internal specialists used through child-session delegation:
+  `bio-methodologist` for computational design / QC / statistics planning
+  `wet-lab-designer` for user-executed wet-lab validation planning
+  `paper-evidence-synthesizer` for cross-paper evidence matrix and confidence grading
+
+This is not limited to generic "analysis". The intended workflow includes:
+
+- literature retrieval
+- public dataset discovery
+- computational analysis
+- wet-lab validation design for the user to execute
+- evidence integration
+- specialist reporting
+
+## Built-in Skill Direction
+
+The built-in skill set now covers both general and bio workflows.
+
+Examples:
+
+- browser / UI / git:
+  - `playwright`
+  - `frontend-ui-ux`
+  - `git-master`
+- document / report:
+  - `docx-workbench`
+  - `pdf-toolkit`
+  - `xlsx-analyst`
+- bioinformatics:
+  - `bio-tools`
+  - `bio-methods`
+  - `wet-lab-design`
+  - `bio-pipeline`
+- `paper-evidence`
+- `differential-expression`
+- `scrna-preprocessing`
+- `cell-annotation`
+- `pubmed-search`
+- `geo-query`
+- `sequence-analysis`
+- `structural-biology`
+- `bio-visualization`
+- `vector-design`
+
+The bio skills are written as execution-oriented references: they specify
+preferred tools, typical commands/code paths, expected artifacts, and boundary
+conditions rather than acting as vague prompt decoration.
+
+Bio agents now also carry explicit data-interaction and environment-safety behavior:
+
+- they ask users for the minimum decisive data when company or sequencing data is missing
+- they separate required inputs from optional context
+- they prefer `uv` for Python environments
+- they prefer `conda` for mixed native stacks
+- they call out when Windows users realistically need WSL/Linux
+
+## Current MCP Set
+
+The built-in MCP surface is intentionally tighter now.
+
+Default built-ins kept visible:
+
+- `websearch`
+- `context7`
+- `grep_app`
+- `browser_puppeteer`
+- `chrome-devtools-mcp`
+- `deepwiki_mcp` (default off)
+- `open_websearch_mcp`
+- `paper_search_mcp`
+- `semantic_scholar_fastmcp`
+
+Removed from the built-in visible set:
+
+- `arxiv_mcp`
+- `fetch_browser`
+
+Rationale:
+
+- avoid duplicate capability surfaces
+- keep the MCP list focused
+- leave `deepwiki_mcp` opt-in instead of always-on
+
+## OpenCode Compatibility Work
+
+Recent migration work has focused on keeping pace with newer OpenCode behavior.
+
+Already aligned or hardened:
+
+- runtime plugin config discovery with canonical + legacy config compatibility
+- agent registration and protected builtin-agent override handling
+- command discovery:
+  - `.opencode/command`
+  - `.opencode/commands`
+  - ancestor discovery up to worktree root
+  - slash-style nested command names
+- `.agents/skills` participation in injection chains
+- MCP merge order and user override behavior
+- todo continuation / compaction / stagnation guard regressions
+
+The migration audit reference lives at:
+
+- [docs/release/upstream-oh-my-openagent-3.11-plus-audit.md](docs/release/upstream-oh-my-openagent-3.11-plus-audit.md)
+
+## Installation Reality
+
+This project is still optimized for local-first use.
+
+Recommended workflow:
+
+```bash
+bun run build:skills-catalog
+bun run build
+bun pm pack
+```
+
+Then follow:
+
+- [docs/guide/installation.md](docs/guide/installation.md)
+
+## Reference Repos
+
+Local comparison material is kept under `Future/` for migration and design work.
+
+Current references include:
+
+- upstream `oh-my-openagent`
+- `BioClaw`
+- `Geneclaw`
+- `codex-main`
+
+These are local reference trees, not part of the shipped plugin.
+
+## Current Priorities
+
+The near-term order is:
+
+1. finish upstream OpenCode compatibility migration
+2. strengthen engineering execution/orchestration capability in core agents
+3. continue refining the bioinformatics agent + skill stack
+
+## Docs
+
+- [docs/guide/installation.md](docs/guide/installation.md)
+- [docs/guide/orchestration.md](docs/guide/orchestration.md)
+- [docs/guide/bio-skills.md](docs/guide/bio-skills.md)
+- [docs/guide/bio-paper-autonomous-flow-v1.md](docs/guide/bio-paper-autonomous-flow-v1.md)
+- [docs/reference/configuration.md](docs/reference/configuration.md)
+- [docs/reference/features.md](docs/reference/features.md)
+
+## Language Versions
+
+- [English](README.md)
+- [简体中文](README.zh-cn.md)
+- [日本語](README.ja.md)
+- [한국어](README.ko.md)
+- [Русский](README.ru.md)