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brain-researcher-coder

v0.0.10

Published

Brain Researcher Coder - neuroimaging AI coding assistant

Readme

Claude Code — Source Code

The full source code of Anthropic's Claude Code CLI, made public on March 31, 2026

TypeScript Bun React + Ink Files MCP Server npm

The original unmodified source is preserved in the backup branch.


Table of Contents


How It Became Public

Chaofan Shou (@Fried_rice) discovered that the published npm package for Claude Code included a .map file referencing the full, unobfuscated TypeScript source — accessible as a zip from Anthropic's R2 storage bucket.

An Anthropic employee subsequently made the source available in the public domain on March 31, 2026.


What Is Claude Code?

Claude Code is Anthropic's official CLI tool for interacting with Claude directly from the terminal — editing files, running commands, searching codebases, managing git workflows, and more. This repository contains the src/ directory.

| | | |---|---| | Published | 2026-03-31 | | Language | TypeScript (strict) | | Runtime | Bun | | Terminal UI | React + Ink | | Scale | ~1,900 files · 512,000+ lines of code |


Install Brain Researcher CLI

The Brain Researcher npm package is published as brain-researcher-coder and installs the br-code command:

npm install -g brain-researcher-coder

If you are using the default local Brain Researcher stack, add your MCP token to your shell profile and reload it:

# ~/.bashrc or ~/.zshrc
export BR_MCP_TOKEN="your-token-here"

source ~/.bashrc

Then start the CLI:

br-code

If you are not using the default local backend, also set your model backend explicitly:

export ANTHROPIC_BASE_URL="http://localhost:4001"
export ANTHROPIC_API_KEY="sk-br-local"
export BR_MCP_TOKEN="your-token-here"

📚 Documentation

For in-depth guides, see the docs/ directory:

| Guide | Description | |-------|-------------| | Architecture | Core pipeline, startup sequence, state management, rendering, data flow | | Tools Reference | Complete catalog of all ~40 agent tools with categories and permission model | | Commands Reference | All ~85 slash commands organized by category | | Subsystems Guide | Deep dives into Bridge, MCP, Permissions, Plugins, Skills, Tasks, Memory, Voice | | Exploration Guide | How to navigate the codebase — study paths, grep patterns, key files |

Also see: CONTRIBUTING.md · MCP Server README


🔍 Explore with MCP Server

This repo ships an MCP server that lets any MCP-compatible client (Claude Code, Claude Desktop, VS Code Copilot, Cursor) explore the full source interactively.

Install from npm

The MCP server is published as claude-code-explorer-mcp on npm — no need to clone the repo:

# Claude Code
claude mcp add claude-code-explorer -- npx -y claude-code-explorer-mcp

One-liner setup (from source)

git clone https://github.com/nirholas/claude-code.git ~/claude-code \
  && cd ~/claude-code/mcp-server \
  && npm install && npm run build \
  && claude mcp add claude-code-explorer -- node ~/claude-code/mcp-server/dist/index.js
# 1. Clone the repo
git clone https://github.com/nirholas/claude-code.git
cd claude-code/mcp-server

# 2. Install & build
npm install && npm run build

# 3. Register with Claude Code
claude mcp add claude-code-explorer -- node /absolute/path/to/claude-code/mcp-server/dist/index.js

Replace /absolute/path/to/claude-code with your actual clone path.

VS Code — add to .vscode/mcp.json:

{
  "servers": {
    "claude-code-explorer": {
      "type": "stdio",
      "command": "node",
      "args": ["${workspaceFolder}/mcp-server/dist/index.js"],
      "env": { "CLAUDE_CODE_SRC_ROOT": "${workspaceFolder}/src" }
    }
  }
}

Claude Desktop — add to your config file:

{
  "mcpServers": {
    "claude-code-explorer": {
      "command": "node",
      "args": ["/absolute/path/to/claude-code/mcp-server/dist/index.js"],
      "env": { "CLAUDE_CODE_SRC_ROOT": "/absolute/path/to/claude-code/src" }
    }
  }
}

Cursor — add to ~/.cursor/mcp.json (same format as Claude Desktop).

Available tools & prompts

| Tool | Description | |------|-------------| | list_tools | List all ~40 agent tools with source files | | list_commands | List all ~50 slash commands with source files | | get_tool_source | Read full source of any tool (e.g. BashTool, FileEditTool) | | get_command_source | Read source of any slash command (e.g. review, mcp) | | read_source_file | Read any file from src/ by path | | search_source | Grep across the entire source tree | | list_directory | Browse src/ directories | | get_architecture | High-level architecture overview |

| Prompt | Description | |--------|-------------| | explain_tool | Deep-dive into how a specific tool works | | explain_command | Understand a slash command's implementation | | architecture_overview | Guided tour of the full architecture | | how_does_it_work | Explain any subsystem (permissions, MCP, bridge, etc.) | | compare_tools | Side-by-side comparison of two tools |

Try asking: "How does the BashTool work?" · "Search for where permissions are checked" · "Show me the /review command source"

Custom source path / Remove

# Custom source location
claude mcp add claude-code-explorer -e CLAUDE_CODE_SRC_ROOT=/path/to/src -- node /path/to/mcp-server/dist/index.js

# Remove
claude mcp remove claude-code-explorer

Directory Structure

src/
├── main.tsx                 # Entrypoint — Commander.js CLI parser + React/Ink renderer
├── QueryEngine.ts           # Core LLM API caller (~46K lines)
├── Tool.ts                  # Tool type definitions (~29K lines)
├── commands.ts              # Command registry (~25K lines)
├── tools.ts                 # Tool registry
├── context.ts               # System/user context collection
├── cost-tracker.ts          # Token cost tracking
│
├── tools/                   # Agent tool implementations (~40)
├── commands/                # Slash command implementations (~50)
├── components/              # Ink UI components (~140)
├── services/                # External service integrations
├── hooks/                   # React hooks (incl. permission checks)
├── types/                   # TypeScript type definitions
├── utils/                   # Utility functions
├── screens/                 # Full-screen UIs (Doctor, REPL, Resume)
│
├── bridge/                  # IDE integration (VS Code, JetBrains)
├── coordinator/             # Multi-agent orchestration
├── plugins/                 # Plugin system
├── skills/                  # Skill system
├── server/                  # Server mode
├── remote/                  # Remote sessions
├── memdir/                  # Persistent memory directory
├── tasks/                   # Task management
├── state/                   # State management
│
├── voice/                   # Voice input
├── vim/                     # Vim mode
├── keybindings/             # Keybinding configuration
├── schemas/                 # Config schemas (Zod)
├── migrations/              # Config migrations
├── entrypoints/             # Initialization logic
├── query/                   # Query pipeline
├── ink/                     # Ink renderer wrapper
├── buddy/                   # Companion sprite (Easter egg 🐣)
├── native-ts/               # Native TypeScript utils
├── outputStyles/            # Output styling
└── upstreamproxy/           # Proxy configuration

Architecture

1. Tool System

src/tools/ — Every tool Claude can invoke is a self-contained module with its own input schema, permission model, and execution logic.

| Tool | Description | |---|---| | File I/O | | | FileReadTool | Read files (images, PDFs, notebooks) | | FileWriteTool | Create / overwrite files | | FileEditTool | Partial modification (string replacement) | | NotebookEditTool | Jupyter notebook editing | | Search | | | GlobTool | File pattern matching | | GrepTool | ripgrep-based content search | | WebSearchTool | Web search | | WebFetchTool | Fetch URL content | | Execution | | | BashTool | Shell command execution | | SkillTool | Skill execution | | MCPTool | MCP server tool invocation | | LSPTool | Language Server Protocol integration | | Agents & Teams | | | AgentTool | Sub-agent spawning | | SendMessageTool | Inter-agent messaging | | TeamCreateTool / TeamDeleteTool | Team management | | TaskCreateTool / TaskUpdateTool | Task management | | Mode & State | | | EnterPlanModeTool / ExitPlanModeTool | Plan mode toggle | | EnterWorktreeTool / ExitWorktreeTool | Git worktree isolation | | ToolSearchTool | Deferred tool discovery | | SleepTool | Proactive mode wait | | CronCreateTool | Scheduled triggers | | RemoteTriggerTool | Remote trigger | | SyntheticOutputTool | Structured output generation |

2. Command System

src/commands/ — User-facing slash commands invoked with / in the REPL.

| Command | Description | | Command | Description | |---|---|---|---|---| | /commit | Git commit | | /memory | Persistent memory | | /review | Code review | | /skills | Skill management | | /compact | Context compression | | /tasks | Task management | | /mcp | MCP server management | | /vim | Vim mode toggle | | /config | Settings | | /diff | View changes | | /doctor | Environment diagnostics | | /cost | Check usage cost | | /login / /logout | Auth | | /theme | Change theme | | /context | Context visualization | | /share | Share session | | /pr_comments | PR comments | | /resume | Restore session | | /desktop | Desktop handoff | | /mobile | Mobile handoff |

3. Service Layer

src/services/ — External integrations and core infrastructure.

| Service | Description | |---|---| | api/ | Anthropic API client, file API, bootstrap | | mcp/ | Model Context Protocol connection & management | | oauth/ | OAuth 2.0 authentication | | lsp/ | Language Server Protocol manager | | analytics/ | GrowthBook feature flags & analytics | | plugins/ | Plugin loader | | compact/ | Conversation context compression | | extractMemories/ | Automatic memory extraction | | teamMemorySync/ | Team memory synchronization | | tokenEstimation.ts | Token count estimation | | policyLimits/ | Organization policy limits | | remoteManagedSettings/ | Remote managed settings |

4. Bridge System

src/bridge/ — Bidirectional communication layer connecting IDE extensions (VS Code, JetBrains) with the CLI.

Key files: bridgeMain.ts (main loop) · bridgeMessaging.ts (protocol) · bridgePermissionCallbacks.ts (permission callbacks) · replBridge.ts (REPL session) · jwtUtils.ts (JWT auth) · sessionRunner.ts (session execution)

5. Permission System

src/hooks/toolPermission/ — Checks permissions on every tool invocation.

Prompts the user for approval/denial or auto-resolves based on the configured permission mode: default, plan, bypassPermissions, auto, etc.

6. Feature Flags

Dead code elimination at build time via Bun's bun:bundle:

import { feature } from 'bun:bundle'

const voiceCommand = feature('VOICE_MODE')
  ? require('./commands/voice/index.js').default
  : null

Notable flags: PROACTIVE · KAIROS · BRIDGE_MODE · DAEMON · VOICE_MODE · AGENT_TRIGGERS · MONITOR_TOOL


Key Files

| File | Lines | Purpose | |------|------:|---------| | QueryEngine.ts | ~46K | Core LLM API engine — streaming, tool loops, thinking mode, retries, token counting | | Tool.ts | ~29K | Base types/interfaces for all tools — input schemas, permissions, progress state | | commands.ts | ~25K | Command registration & execution with conditional per-environment imports | | main.tsx | — | CLI parser + React/Ink renderer; parallelizes MDM, keychain, and GrowthBook on startup |


Tech Stack

| Category | Technology | |---|---| | Runtime | Bun | | Language | TypeScript (strict) | | Terminal UI | React + Ink | | CLI Parsing | Commander.js (extra-typings) | | Schema Validation | Zod v4 | | Code Search | ripgrep (via GrepTool) | | Protocols | MCP SDK · LSP | | API | Anthropic SDK | | Telemetry | OpenTelemetry + gRPC | | Feature Flags | GrowthBook | | Auth | OAuth 2.0 · JWT · macOS Keychain |


Design Patterns

MDM settings, keychain reads, and API preconnect fire in parallel as side-effects before heavy module evaluation:

// main.tsx
startMdmRawRead()
startKeychainPrefetch()

OpenTelemetry (~400KB) and gRPC (~700KB) are loaded via dynamic import() only when needed.

Sub-agents spawn via AgentTool, with coordinator/ handling orchestration. TeamCreateTool enables team-level parallel work.

Defined in skills/ and executed through SkillTool. Users can add custom skills.

Built-in and third-party plugins loaded through the plugins/ subsystem.


GitPretty Setup

# Apply emoji commits
bash ./gitpretty-apply.sh .

# Optional: install hooks for future commits
bash ./gitpretty-apply.sh . --hooks

# Push as usual
git push origin main

Contributing

Contributions to documentation, the MCP server, and exploration tooling are welcome. See CONTRIBUTING.md for guidelines.

Note: The src/ directory is the original source and should not be modified.


Disclaimer

This repository contains source code from Anthropic's Claude Code, made publicly available on 2026-03-31. All original source code is the property of Anthropic. Contact nichxbt for any questions or comments.