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README: move Directory Reference above Architecture Overview
Co-Authored-By: Claude Opus 4.6 <[email protected]>
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‎README.md‎

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@@ -58,6 +58,139 @@ please contact the repository owner for immediate removal.
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## Directory Reference
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```
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src/
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├── main.tsx # REPL bootstrap, 4,683 lines
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├── QueryEngine.ts # SDK/headless query lifecycle engine
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├── query.ts # Main agent loop (785KB, largest file)
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├── Tool.ts # Tool interface + buildTool factory
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├── Task.ts # Task types, IDs, state base
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├── tools.ts # Tool registry, presets, filtering
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├── commands.ts # Slash command definitions
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├── context.ts # User input context
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├── cost-tracker.ts # API cost accumulation
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├── setup.ts # First-run setup flow
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│
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├── bridge/ # Claude Desktop / remote bridge
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│ ├── bridgeMain.ts # Session lifecycle manager
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│ ├── bridgeApi.ts # HTTP client
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│ ├── bridgeConfig.ts # Connection config
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│ ├── bridgeMessaging.ts # Message relay
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│ ├── sessionRunner.ts # Process spawning
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│ ├── jwtUtils.ts # JWT refresh
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│ ├── workSecret.ts # Auth tokens
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│ └── capacityWake.ts # Capacity-based wakeup
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│
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├── cli/ # CLI infrastructure
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│ ├── handlers/ # Command handlers
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│ └── transports/ # I/O transports (stdio, structured)
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│
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├── commands/ # ~80 slash commands
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│ ├── agents/ # Agent management
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│ ├── compact/ # Context compaction
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│ ├── config/ # Settings management
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│ ├── help/ # Help display
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│ ├── login/ # Authentication
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│ ├── mcp/ # MCP server management
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│ ├── memory/ # Memory system
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│ ├── plan/ # Plan mode
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│ ├── resume/ # Session resume
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│ ├── review/ # Code review
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│ └── ... # 70+ more commands
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│
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├── components/ # React/Ink terminal UI
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│ ├── design-system/ # Reusable UI primitives
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│ ├── messages/ # Message rendering
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│ ├── permissions/ # Permission dialogs
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│ ├── PromptInput/ # Input field + suggestions
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│ ├── LogoV2/ # Branding + welcome screen
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│ ├── Settings/ # Settings panels
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│ ├── Spinner.tsx # Loading indicators
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│ └── ... # 40+ component groups
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│
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├── entrypoints/ # Application entry points
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│ ├── cli.tsx # CLI main (version, help, daemon)
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│ ├── sdk/ # Agent SDK (types, sessions)
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│ └── mcp.ts # MCP server entry
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│
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├── hooks/ # React hooks
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│ ├── useCanUseTool.tsx # Permission checking
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│ ├── useReplBridge.tsx # Bridge connection
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│ ├── notifs/ # Notification hooks
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│ └── toolPermission/ # Tool permission handlers
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│
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├── services/ # Business logic layer
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│ ├── api/ # Claude API client
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│ │ ├── claude.ts # Streaming API calls
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│ │ ├── errors.ts # Error categorization
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│ │ └── withRetry.ts # Retry logic
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│ ├── analytics/ # Telemetry + GrowthBook
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│ ├── compact/ # Context compression
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│ ├── mcp/ # MCP connection management
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│ ├── tools/ # Tool execution engine
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│ │ ├── StreamingToolExecutor.ts # Parallel tool runner
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│ │ └── toolOrchestration.ts # Batch orchestration
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│ ├── plugins/ # Plugin loader
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│ └── settingsSync/ # Cross-device settings
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│
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├── state/ # Application state
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│ ├── AppStateStore.ts # Store definition
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│ └── AppState.tsx # React provider + hooks
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│
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├── tasks/ # Task implementations
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│ ├── LocalShellTask/ # Bash command execution
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│ ├── LocalAgentTask/ # Sub-agent execution
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│ ├── RemoteAgentTask/ # Remote agent via bridge
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│ ├── InProcessTeammateTask/ # In-process teammate
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│ └── DreamTask/ # Background thinking
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│
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├── tools/ # 40+ tool implementations
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│ ├── AgentTool/ # Sub-agent spawning + fork
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│ ├── BashTool/ # Shell command execution
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│ ├── FileReadTool/ # File reading (PDF, image, etc)
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│ ├── FileEditTool/ # String-replace editing
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│ ├── FileWriteTool/ # Full file creation
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│ ├── GlobTool/ # File pattern search
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│ ├── GrepTool/ # Content search (ripgrep)
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│ ├── WebFetchTool/ # HTTP fetching
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│ ├── WebSearchTool/ # Web search
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│ ├── MCPTool/ # MCP tool wrapper
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│ ├── SkillTool/ # Skill invocation
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│ ├── AskUserQuestionTool/ # User interaction
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│ └── ... # 30+ more tools
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│
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├── types/ # Type definitions
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│ ├── message.ts # Message discriminated unions
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│ ├── permissions.ts # Permission types
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│ ├── tools.ts # Tool progress types
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│ └── ids.ts # Branded ID types
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│
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├── utils/ # Utilities (largest directory)
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│ ├── permissions/ # Permission rule engine
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│ ├── messages/ # Message formatting
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│ ├── model/ # Model selection logic
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│ ├── settings/ # Settings management
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│ ├── sandbox/ # Sandbox runtime adapter
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│ ├── hooks/ # Hook execution
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│ ├── memory/ # Memory system utils
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│ ├── git/ # Git operations
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│ ├── github/ # GitHub API
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│ ├── bash/ # Bash execution helpers
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│ ├── swarm/ # Multi-agent swarm
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│ ├── telemetry/ # Telemetry reporting
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│ └── ... # 30+ more util groups
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│
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└── vendor/ # Native module source stubs
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├── audio-capture-src/ # Audio input
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├── image-processor-src/ # Image processing
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├── modifiers-napi-src/ # Native modifiers
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└── url-handler-src/ # URL handling
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```
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---
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## Architecture Overview
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```
@@ -601,139 +734,6 @@ This source code demonstrates 12 layered mechanisms that a production AI agent h
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## Directory Reference
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```
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src/
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├── main.tsx # REPL bootstrap, 4,683 lines
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├── QueryEngine.ts # SDK/headless query lifecycle engine
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├── query.ts # Main agent loop (785KB, largest file)
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├── Tool.ts # Tool interface + buildTool factory
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├── Task.ts # Task types, IDs, state base
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├── tools.ts # Tool registry, presets, filtering
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├── commands.ts # Slash command definitions
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├── context.ts # User input context
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├── cost-tracker.ts # API cost accumulation
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├── setup.ts # First-run setup flow
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│
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├── bridge/ # Claude Desktop / remote bridge
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│ ├── bridgeMain.ts # Session lifecycle manager
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│ ├── bridgeApi.ts # HTTP client
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│ ├── bridgeConfig.ts # Connection config
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│ ├── bridgeMessaging.ts # Message relay
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│ ├── sessionRunner.ts # Process spawning
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│ ├── jwtUtils.ts # JWT refresh
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│ ├── workSecret.ts # Auth tokens
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│ └── capacityWake.ts # Capacity-based wakeup
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│
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├── cli/ # CLI infrastructure
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│ ├── handlers/ # Command handlers
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│ └── transports/ # I/O transports (stdio, structured)
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│
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├── commands/ # ~80 slash commands
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│ ├── agents/ # Agent management
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│ ├── compact/ # Context compaction
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│ ├── config/ # Settings management
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│ ├── help/ # Help display
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│ ├── login/ # Authentication
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│ ├── mcp/ # MCP server management
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│ ├── memory/ # Memory system
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│ ├── plan/ # Plan mode
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│ ├── resume/ # Session resume
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│ ├── review/ # Code review
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│ └── ... # 70+ more commands
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│
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├── components/ # React/Ink terminal UI
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│ ├── design-system/ # Reusable UI primitives
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│ ├── messages/ # Message rendering
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│ ├── permissions/ # Permission dialogs
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│ ├── PromptInput/ # Input field + suggestions
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│ ├── LogoV2/ # Branding + welcome screen
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│ ├── Settings/ # Settings panels
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│ ├── Spinner.tsx # Loading indicators
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│ └── ... # 40+ component groups
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│
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├── entrypoints/ # Application entry points
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│ ├── cli.tsx # CLI main (version, help, daemon)
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│ ├── sdk/ # Agent SDK (types, sessions)
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│ └── mcp.ts # MCP server entry
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│
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├── hooks/ # React hooks
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│ ├── useCanUseTool.tsx # Permission checking
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│ ├── useReplBridge.tsx # Bridge connection
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│ ├── notifs/ # Notification hooks
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│ └── toolPermission/ # Tool permission handlers
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│
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├── services/ # Business logic layer
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│ ├── api/ # Claude API client
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│ │ ├── claude.ts # Streaming API calls
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│ │ ├── errors.ts # Error categorization
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│ │ └── withRetry.ts # Retry logic
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│ ├── analytics/ # Telemetry + GrowthBook
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│ ├── compact/ # Context compression
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│ ├── mcp/ # MCP connection management
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│ ├── tools/ # Tool execution engine
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│ │ ├── StreamingToolExecutor.ts # Parallel tool runner
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│ │ └── toolOrchestration.ts # Batch orchestration
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│ ├── plugins/ # Plugin loader
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│ └── settingsSync/ # Cross-device settings
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│
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├── state/ # Application state
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│ ├── AppStateStore.ts # Store definition
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│ └── AppState.tsx # React provider + hooks
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│
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├── tasks/ # Task implementations
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│ ├── LocalShellTask/ # Bash command execution
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│ ├── LocalAgentTask/ # Sub-agent execution
688-
│ ├── RemoteAgentTask/ # Remote agent via bridge
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│ ├── InProcessTeammateTask/ # In-process teammate
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│ └── DreamTask/ # Background thinking
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│
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├── tools/ # 40+ tool implementations
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│ ├── AgentTool/ # Sub-agent spawning + fork
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│ ├── BashTool/ # Shell command execution
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│ ├── FileReadTool/ # File reading (PDF, image, etc)
696-
│ ├── FileEditTool/ # String-replace editing
697-
│ ├── FileWriteTool/ # Full file creation
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│ ├── GlobTool/ # File pattern search
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│ ├── GrepTool/ # Content search (ripgrep)
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│ ├── WebFetchTool/ # HTTP fetching
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│ ├── WebSearchTool/ # Web search
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│ ├── MCPTool/ # MCP tool wrapper
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│ ├── SkillTool/ # Skill invocation
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│ ├── AskUserQuestionTool/ # User interaction
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│ └── ... # 30+ more tools
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│
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├── types/ # Type definitions
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│ ├── message.ts # Message discriminated unions
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│ ├── permissions.ts # Permission types
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│ ├── tools.ts # Tool progress types
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│ └── ids.ts # Branded ID types
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│
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├── utils/ # Utilities (largest directory)
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│ ├── permissions/ # Permission rule engine
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│ ├── messages/ # Message formatting
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│ ├── model/ # Model selection logic
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│ ├── settings/ # Settings management
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│ ├── sandbox/ # Sandbox runtime adapter
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│ ├── hooks/ # Hook execution
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│ ├── memory/ # Memory system utils
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│ ├── git/ # Git operations
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│ ├── github/ # GitHub API
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│ ├── bash/ # Bash execution helpers
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│ ├── swarm/ # Multi-agent swarm
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│ ├── telemetry/ # Telemetry reporting
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│ └── ... # 30+ more util groups
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│
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└── vendor/ # Native module source stubs
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├── audio-capture-src/ # Audio input
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├── image-processor-src/ # Image processing
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├── modifiers-napi-src/ # Native modifiers
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└── url-handler-src/ # URL handling
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```
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---
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## Build Notes
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This source is **not directly compilable** from this repo alone:

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