refactor(coding-agent): flattened directory structure, eliminated core/ folder

- Eliminated core/ directory (252 files, 23 subdirs → distributed) - Reduced max nesting from 9 levels to 5 levels - Promoted tool subdirs to top level: exa/, lsp/, patch/, task/, web/ - Merged web-scrapers/ + web-search/ into web/{scrapers,search}/ - Flattened modes/interactive/ to modes/ - Split execution/ into: ipy/ (python), exec/ (bash), ssh/ - Renamed ipy/python-*.ts to ipy/*.ts (executor, kernel, etc.) - Flattened cursor/exec-bridge.ts to cursor.ts - Created logical groupings: config/, session/, extensibility/, export/ - Updated all imports across 500+ files
2026-01-23 12:05:24 +01:00
parent 7b5af2dd9f
commit cb5bbbf382
531 changed files with 1316 additions and 1322 deletions
@@ -15,14 +15,14 @@ The coding-agent is structured into distinct layers:
                              ▼
 ┌─────────────────────────────────────────────────────────────┐
 │                       Mode Layer                            │
-│  modes/interactive/   modes/print-mode.ts   modes/rpc/     │
+│  modes/interactive-mode.ts   modes/print-mode.ts   modes/rpc/│
 └─────────────────────────────────────────────────────────────┘
                              │
                              ▼
 ┌─────────────────────────────────────────────────────────────┐
 │                       Core Layer                            │
-│  core/agent-session.ts, core/sdk.ts (SDK wrapper)          │
-│  core/session-manager.ts, core/model-resolver.ts, etc.     │
+│  session/agent-session.ts, sdk.ts (SDK wrapper)            │
+│  session/session-manager.ts, config/model-resolver.ts, etc.│
 └─────────────────────────────────────────────────────────────┘
                              │
                              ▼
@@ -43,6 +43,9 @@ src/
 ├── index.ts                  # Public API exports (SDK)
 ├── config.ts                 # APP_NAME, VERSION, paths (getAgentDir, etc.)
 ├── migrations.ts             # Session/config migration logic
+├── sdk.ts                    # SDK wrapper for programmatic usage
+├── system-prompt.ts          # buildSystemPrompt(), loadProjectContextFiles()
+├── cursor.ts                 # Cursor exec bridge (flattened from execution/cursor/)

 ├── cli/                      # CLI-specific utilities
 │   ├── args.ts               # parseArgs(), printHelp(), Args interface
@@ -66,6 +69,13 @@ src/
 │   ├── system-prompt.ts      # System prompt capability
 │   └── tool.ts               # Tool capability

+├── config/                   # Configuration management
+│   ├── keybindings.ts        # Keybinding configuration
+│   ├── model-registry.ts     # Model registry and configuration
+│   ├── model-resolver.ts     # resolveModelScope(), restoreModelFromSession()
+│   ├── prompt-templates.ts   # Prompt template loading and rendering
+│   └── settings-manager.ts   # SettingsManager class - user preferences
+
 ├── discovery/                # Extension discovery from multiple sources
 │   ├── index.ts              # Main discovery orchestration
 │   ├── builtin.ts            # Built-in extensions
@@ -80,41 +90,30 @@ src/
 │   ├── windsurf.ts           # Windsurf discovery
 │   └── helpers.ts            # Discovery helper functions

-├── prompts/                  # Prompt templates
-│   ├── system-prompt.md      # Main system prompt
-│   ├── task.md               # Task agent prompt
-│   ├── init.md               # Initialization prompt
-│   ├── compaction-*.md       # Compaction prompts
-│   └── tools/                # Tool-specific prompts
+├── exa/                      # Exa MCP tools (22 tools)
+│   ├── index.ts              # Exa tools exports
+│   ├── company.ts            # Company search
+│   ├── linkedin.ts           # LinkedIn search
+│   ├── mcp-client.ts         # MCP client for Exa
+│   ├── render.ts             # Exa result rendering
+│   ├── researcher.ts         # Research tools
+│   ├── search.ts             # Search tools
+│   ├── types.ts              # Exa types
+│   └── websets.ts            # Websets tools

-├── core/                     # Core business logic (mode-agnostic)
-│   ├── index.ts              # Core exports
-│   ├── agent-session.ts      # AgentSession class - THE central abstraction
-│   ├── sdk.ts                # SDK wrapper for programmatic usage
-│   ├── auth-storage.ts       # AuthStorage class - API keys and OAuth tokens
+├── exec/                     # Bash/shell execution
 │   ├── bash-executor.ts      # executeBash() with streaming, abort
-│   ├── event-bus.ts          # Event bus for tool communication
-│   ├── exec.ts               # Process execution utilities
-│   ├── file-mentions.ts      # File mention detection
-│   ├── keybindings.ts        # Keybinding configuration
-│   ├── logger.ts             # Winston-based logging
-│   ├── messages.ts           # BashExecutionMessage, messageTransformer
-│   ├── model-registry.ts     # Model registry and configuration
-│   ├── model-resolver.ts     # resolveModelScope(), restoreModelFromSession()
-│   ├── prompt-templates.ts   # Prompt template loading and rendering
-│   ├── session-manager.ts    # SessionManager class - JSONL persistence
-│   ├── settings-manager.ts   # SettingsManager class - user preferences
-│   ├── skills.ts             # loadSkills(), skill discovery from multiple locations
-│   ├── slash-commands.ts     # loadSlashCommands() from ~/.omp/agent/commands/
-│   ├── system-prompt.ts      # buildSystemPrompt(), loadProjectContextFiles()
-│   ├── terminal-notify.ts    # Terminal notification utilities
-│   ├── timings.ts            # Performance timing utilities
-│   ├── title-generator.ts    # Session title generation
+│   └── exec.ts               # Process execution utilities
+
+├── export/                   # Export functionality
+│   ├── custom-share.ts       # Custom sharing
 │   ├── ttsr.ts               # Text-to-speech/speech-to-text utilities
-│   ├── utils.ts              # Generic utilities
-│   │
-│   ├── compaction/           # Context compaction system
-│   │   └── index.ts          # Compaction logic, summary generation
+│   └── html/                 # Session export to HTML
+│       └── index.ts          # HTML export logic
+
+├── extensibility/            # Extension and customization systems
+│   ├── skills.ts             # loadSkills(), skill discovery
+│   ├── slash-commands.ts     # loadSlashCommands()
 │   │
 │   ├── custom-commands/      # Custom command loading system
 │   │   └── types.ts          # CustomCommand types
@@ -122,114 +121,213 @@ src/
 │   ├── custom-tools/         # Custom tool loading system
 │   │   ├── index.ts          # Custom tool exports
 │   │   ├── types.ts          # CustomToolFactory, CustomToolDefinition
-│   │   ├── loader.ts         # loadCustomTools() from multiple locations
+│   │   ├── loader.ts         # loadCustomTools()
 │   │   └── wrapper.ts        # Tool wrapper utilities
 │   │
-│   ├── export-html/          # Session export to HTML
-│   │   └── (export logic)
-│   │
 │   ├── extensions/           # Extension system
-│   │   └── (extension loading and execution)
+│   │   ├── index.ts          # Extension exports
+│   │   ├── types.ts          # Extension types
+│   │   ├── loader.ts         # Extension loading
+│   │   ├── runner.ts         # Extension event dispatch
+│   │   └── wrapper.ts        # Extension wrappers
 │   │
-│   ├── hooks/                # Hook system for extending behavior
+│   ├── hooks/                # Hook system
 │   │   ├── index.ts          # Hook exports
 │   │   ├── types.ts          # HookAPI, HookContext, event types
-│   │   ├── loader.ts         # loadHooks() from multiple locations
-│   │   ├── runner.ts         # runHook() event dispatch
-│   │   └── tool-wrapper.ts   # wrapToolsWithHooks() for tool_call events
+│   │   ├── loader.ts         # loadHooks()
+│   │   └── runner.ts         # runHook() event dispatch
 │   │
-│   ├── mcp/                  # MCP (Model Context Protocol) integration
-│   │   └── (MCP client/server logic)
-│   │
-│   ├── plugins/              # Plugin system
-│   │   └── (plugin loading and management)
-│   │
-│   └── tools/                # Built-in tool implementations
-│       ├── index.ts          # Tool exports, BUILTIN_TOOLS, createTools
-│       ├── ask.ts            # User input tool
-│       ├── bash.ts           # Bash command execution
-│       ├── bash-interceptor.ts # Bash command interception
-│       ├── context.ts        # Tool context utilities
-│       ├── edit.ts           # Surgical file editing
-│       ├── edit-diff.ts      # Diff-based editing
-│       ├── find.ts           # File search by glob
-│       ├── gemini-image.ts   # Gemini image generation
-│       ├── git.ts            # Git operations
-│       ├── grep.ts           # Content search (regex/literal)
-│       ├── ls.ts             # Directory listing
-│       ├── notebook.ts       # Jupyter notebook editing
-│       ├── output.ts         # Output/logging tool
-│       ├── read.ts           # File reading (text and images)
-│       ├── review.ts         # Code review tools
-│       ├── rulebook.ts       # Rulebook tool
-│       ├── write.ts          # File writing
-│       ├── fetch.ts          # URL content fetching
-│       ├── exa/              # Exa MCP tools (22 tools)
-│       ├── lsp/              # LSP integration tools
-│       ├── task/             # Task/subagent spawning
-│       ├── web-search/       # Web search tools
-│       ├── path-utils.ts     # Path resolution utilities
-│       ├── renderers.ts      # Tool output renderers
-│       ├── render-utils.ts   # Rendering utilities
-│       └── truncate.ts       # Output truncation utilities
+│   └── plugins/              # Plugin system
+│       └── (plugin loading and management)
+
+├── internal-urls/            # Internal URL protocol handlers
+│   ├── index.ts              # Router and exports
+│   ├── rule-protocol.ts      # Rule protocol handler
+│   └── skill-protocol.ts     # Skill protocol handler
+
+├── ipy/                      # Python/Jupyter execution
+│   ├── executor.ts           # executePython(), kernel execution
+│   ├── gateway-coordinator.ts # Gateway coordination
+│   ├── kernel.ts             # PythonKernel class
+│   ├── modules.ts            # Python module discovery
+│   ├── prelude.ts            # Python prelude (TS bindings)
+│   └── prelude.py            # Python prelude script
+
+├── lsp/                      # LSP integration
+│   ├── index.ts              # LSP exports
+│   ├── client.ts             # LSP client
+│   ├── config.ts             # LSP configuration
+│   ├── render.ts             # LSP result rendering
+│   ├── utils.ts              # LSP utilities
+│   └── clients/              # Language-specific clients
+│       ├── index.ts          # Client exports
+│       ├── biome-client.ts   # Biome LSP
+│       └── lsp-linter-client.ts # Generic linter
+
+├── mcp/                      # MCP (Model Context Protocol) integration
+│   ├── index.ts              # MCP exports
+│   ├── config.ts             # MCP configuration
+│   ├── loader.ts             # MCP server loading
+│   ├── manager.ts            # MCPManager class
+│   ├── tool-bridge.ts        # Tool bridging
+│   ├── tool-cache.ts         # Tool caching
+│   ├── types.ts              # MCP types
+│   └── transports/           # MCP transports
+│       ├── http.ts           # HTTP transport
+│       └── stdio.ts          # Stdio transport

 ├── modes/                    # Run mode implementations
-│   ├── index.ts              # Re-exports InteractiveMode, runPrintMode, runRpcMode, RpcClient
-│   ├── print-mode.ts         # Non-interactive: process messages, print output, exit
+│   ├── index.ts              # Re-exports InteractiveMode, runPrintMode, runRpcMode
+│   ├── interactive-mode.ts   # InteractiveMode class (main TUI)
+│   ├── print-mode.ts         # Non-interactive mode
+│   ├── types.ts              # Mode types
 │   │
-│   ├── rpc/                  # RPC mode for programmatic control
-│   │   ├── rpc-mode.ts       # runRpcMode() - JSON stdin/stdout protocol
-│   │   ├── rpc-types.ts      # RpcCommand, RpcResponse, RpcSessionState types
-│   │   └── rpc-client.ts     # RpcClient class for spawning/controlling agent
+│   ├── components/           # TUI components
+│   │   ├── index.ts          # Component exports
+│   │   ├── assistant-message.ts    # Agent response rendering
+│   │   ├── bash-execution.ts       # Bash output display
+│   │   ├── custom-editor.ts        # Multi-line input editor
+│   │   ├── dynamic-border.ts       # Adaptive border rendering
+│   │   ├── footer.ts               # Status bar / footer
+│   │   ├── hook-input.ts           # Hook input dialog
+│   │   ├── hook-selector.ts        # Hook selection UI
+│   │   ├── login-dialog.ts         # OAuth login dialog
+│   │   ├── model-selector.ts       # Model picker
+│   │   ├── session-selector.ts     # Session browser for --resume
+│   │   ├── theme-selector.ts       # Theme picker
+│   │   ├── thinking-selector.ts    # Thinking level picker
+│   │   ├── tool-execution.ts       # Tool call/result rendering
+│   │   ├── user-message.ts         # User message rendering
+│   │   ├── status-line/            # Status line components
+│   │   └── extensions/             # Extension UI components
 │   │
-│   └── interactive/          # Interactive TUI mode
-│       ├── interactive-mode.ts   # InteractiveMode class
-│       │
-│       ├── components/           # TUI components
-│       │   ├── assistant-message.ts    # Agent response rendering
-│       │   ├── bash-execution.ts       # Bash output display
-│       │   ├── compaction.ts           # Compaction status display
-│       │   ├── countdown-timer.ts      # Reusable countdown for dialogs
-│       │   ├── custom-editor.ts        # Multi-line input editor
-│       │   ├── dynamic-border.ts       # Adaptive border rendering
-│       │   ├── footer.ts               # Status bar / footer
-│       │   ├── hook-input.ts           # Hook input dialog
-│       │   ├── hook-selector.ts        # Hook selection UI
-│       │   ├── index.ts                # Component exports
-│       │   ├── login-dialog.ts         # OAuth login dialog
-│       │   ├── model-selector.ts       # Model picker
-│       │   ├── oauth-selector.ts       # OAuth provider picker
-│       │   ├── queue-mode-selector.ts  # Message queue mode picker
-│       │   ├── session-selector.ts     # Session browser for --resume
-│       │   ├── show-images-selector.ts # Image display toggle
-│       │   ├── theme-selector.ts       # Theme picker
-│       │   ├── thinking-selector.ts    # Thinking level picker
-│       │   ├── tool-execution.ts       # Tool call/result rendering
-│       │   ├── user-message-selector.ts # Message selector for /branch
-│       │   └── user-message.ts         # User message rendering
-│       │
-│       └── theme/
-│           ├── theme.ts      # Theme loading, getEditorTheme(), etc.
-│           ├── dark.json
-│           ├── light.json
-│           └── theme-schema.json
+│   ├── controllers/          # TUI controllers
+│   │   ├── command-controller.ts   # Command handling
+│   │   ├── event-controller.ts     # Event handling
+│   │   ├── input-controller.ts     # Input handling
+│   │   └── selector-controller.ts  # Selector handling
+│   │
+│   ├── theme/                # Theme system
+│   │   ├── theme.ts          # Theme loading, getEditorTheme()
+│   │   └── defaults/         # Default themes
+│   │
+│   ├── utils/                # Mode utilities
+│   │   └── ui-helpers.ts     # UI helper functions
+│   │
+│   └── rpc/                  # RPC mode for programmatic control
+│       ├── rpc-mode.ts       # runRpcMode() - JSON stdin/stdout protocol
+│       ├── rpc-types.ts      # RpcCommand, RpcResponse types
+│       └── rpc-client.ts     # RpcClient class

-└── utils/                    # Generic utilities
-    ├── changelog.ts          # parseChangelog(), getNewEntries()
-    ├── clipboard.ts          # copyToClipboard()
-    ├── fuzzy.ts              # Fuzzy string matching
-    ├── image-convert.ts      # Image format conversion
-    ├── image-magick.ts       # ImageMagick integration
-    ├── image-resize.ts       # Image resizing utilities
-    ├── mime.ts               # MIME type detection
-    ├── shell.ts              # getShellConfig()
-    ├── shell-snapshot.ts     # Shell state snapshotting
-    └── tools-manager.ts      # ensureTool() - download fd, etc.
+├── patch/                    # File patching/editing
+│   ├── index.ts              # EditTool and exports
+│   ├── applicator.ts         # Patch application
+│   ├── diff.ts               # Diff utilities
+│   ├── shared.ts             # Shared utilities
+│   └── render.ts             # Patch rendering
+
+├── prompts/                  # Prompt templates
+│   ├── system/               # System prompts
+│   ├── agents/               # Agent-specific prompts
+│   ├── compaction/           # Compaction prompts
+│   └── tools/                # Tool-specific prompts
+
+├── session/                  # Session management
+│   ├── agent-session.ts      # AgentSession class - THE central abstraction
+│   ├── agent-storage.ts      # Agent storage utilities
+│   ├── auth-storage.ts       # AuthStorage class - API keys and OAuth
+│   ├── artifacts.ts          # Artifact management
+│   ├── history-storage.ts    # History storage
+│   ├── messages.ts           # Message types and transformers
+│   ├── session-manager.ts    # SessionManager class - JSONL persistence
+│   ├── session-storage.ts    # Session storage utilities
+│   ├── storage-migration.ts  # Storage migration
+│   ├── streaming-output.ts   # Streaming output handling
+│   └── compaction/           # Context compaction system
+│       └── index.ts          # Compaction logic, summary generation
+
+├── ssh/                      # SSH execution
+│   ├── connection-manager.ts # SSH connection management
+│   ├── ssh-executor.ts       # executeSSH() with streaming
+│   └── sshfs-mount.ts        # SSHFS mounting
+
+├── task/                     # Task/subagent spawning
+│   ├── index.ts              # TaskTool exports
+│   ├── agents.ts             # Agent definitions
+│   ├── commands.ts           # Task commands
+│   ├── discovery.ts          # Task discovery
+│   ├── executor.ts           # Task execution
+│   ├── render.ts             # Task rendering
+│   ├── subprocess-tool-registry.ts # Subprocess tool registry
+│   ├── worker-protocol.ts    # Worker protocol
+│   └── worker.ts             # Task worker
+
+├── tools/                    # Built-in tool implementations
+│   ├── index.ts              # Tool exports, BUILTIN_TOOLS, createTools
+│   ├── ask.ts                # User input tool
+│   ├── bash.ts               # Bash command execution
+│   ├── bash-interceptor.ts   # Bash command interception
+│   ├── calculator.ts         # Calculator tool
+│   ├── complete.ts           # Completion tool
+│   ├── context.ts            # Tool context utilities
+│   ├── fetch.ts              # URL content fetching
+│   ├── find.ts               # File search by glob
+│   ├── gemini-image.ts       # Gemini image generation
+│   ├── grep.ts               # Content search (regex/literal)
+│   ├── ls.ts                 # Directory listing
+│   ├── notebook.ts           # Jupyter notebook editing
+│   ├── output-meta.ts        # Output metadata
+│   ├── output-utils.ts       # Output utilities
+│   ├── path-utils.ts         # Path resolution utilities
+│   ├── python.ts             # Python tool (delegates to ipy/)
+│   ├── read.ts               # File reading (text and images)
+│   ├── renderers.ts          # Tool output renderers
+│   ├── render-utils.ts       # Rendering utilities
+│   ├── review.ts             # Code review tools
+│   ├── ssh.ts                # SSH tool (delegates to ssh/)
+│   ├── todo-write.ts         # Todo management
+│   ├── tool-errors.ts        # Tool error types
+│   ├── tool-result.ts        # Tool result utilities
+│   ├── truncate.ts           # Output truncation utilities
+│   └── write.ts              # File writing
+
+├── utils/                    # Generic utilities
+│   ├── changelog.ts          # parseChangelog(), getNewEntries()
+│   ├── event-bus.ts          # Event bus for tool communication
+│   ├── file-mentions.ts      # File mention detection
+│   ├── frontmatter.ts        # Frontmatter parsing
+│   ├── image-convert.ts      # Image format conversion
+│   ├── image-resize.ts       # Image resizing utilities
+│   ├── mime.ts               # MIME type detection
+│   ├── shell.ts              # getShellConfig()
+│   ├── terminal-notify.ts    # Terminal notification utilities
+│   ├── timings.ts            # Performance timing utilities
+│   ├── title-generator.ts    # Session title generation
+│   ├── tools-manager.ts      # ensureTool() - download fd, etc.
+│   └── utils.ts              # Generic utilities
+
+├── vendor/                   # Vendored dependencies
+│   └── photon/               # Photon image processing
+
+└── web/                      # Web tools (merged web-scrapers + web-search)
+    ├── scrapers/             # Web scraping
+    │   ├── index.ts          # Scraper exports
+    │   ├── types.ts          # Scraper types
+    │   ├── utils.ts          # Scraper utilities
+    │   └── (domain-specific scrapers)
+    └── search/               # Web search
+        ├── index.ts          # WebSearchTool exports
+        ├── auth.ts           # Search auth
+        ├── render.ts         # Search result rendering
+        └── providers/        # Search providers
+            ├── anthropic.ts  # Anthropic search
+            ├── exa.ts        # Exa search
+            └── perplexity.ts # Perplexity search
 ```

 ## Key Abstractions

-### AgentSession (core/agent-session.ts)
+### AgentSession (session/agent-session.ts)

 The central abstraction that wraps the SDK Agent with:

@@ -245,11 +343,11 @@ The central abstraction that wraps the SDK Agent with:

 All three modes (interactive, print, rpc) use AgentSession.

-### SDK (core/sdk.ts)
+### SDK (sdk.ts)

 Wrapper around `@oh-my-pi/pi-agent-core` that provides a simplified interface for creating and managing agents programmatically. Used by AgentSession and available as a public API through index.ts exports.

-### InteractiveMode (modes/interactive/interactive-mode.ts)
+### InteractiveMode (modes/interactive-mode.ts)

 Handles TUI rendering and user interaction:

@@ -268,7 +366,7 @@ Headless operation via JSON protocol over stdin/stdout:

 The RPC mode exposes the full AgentSession API via JSON commands. See [docs/rpc.md](docs/rpc.md) for protocol documentation.

-### SessionManager (core/session-manager.ts)
+### SessionManager (session/session-manager.ts)

 Handles session persistence:

@@ -277,7 +375,7 @@ Handles session persistence:
 - Message loading/saving
 - Model/thinking level persistence

-### SettingsManager (core/settings-manager.ts)
+### SettingsManager (config/settings-manager.ts)

 Handles user preferences:

@@ -290,13 +388,12 @@ Handles user preferences:
 - Thinking budgets (`thinkingBudgets` setting for custom token budgets per level)
 - Image blocking (`blockImages` setting to prevent images from being sent to LLM)

-### Hook System (core/hooks/)
+### Hook System (extensibility/hooks/)

 Extensibility layer for intercepting agent behavior:

 - **loader.ts**: Discovers and loads hooks from `~/.omp/agent/hooks/`, `.omp/hooks/`, and CLI
 - **runner.ts**: Dispatches events to registered hooks
- **tool-wrapper.ts**: Wraps tools to emit `tool_call` and `tool_result` events
 - **types.ts**: Event types (`session`, `tool_call`, `tool_result`, `message`, `error`, `user_bash`)

 See [docs/hooks.md](docs/hooks.md) for full documentation.
@@ -305,7 +402,7 @@ See [docs/hooks.md](docs/hooks.md) for full documentation.

 The extension system uses a shared runtime pattern:

-1. **ExtensionRuntime** (`core/extensions/types.ts`): Shared state and action handlers for all extensions
+1. **ExtensionRuntime** (`extensibility/extensions/types.ts`): Shared state and action handlers for all extensions
 2. **Extension**: Per-extension registration data (handlers, tools, commands, shortcuts)
 3. **ExtensionAPI**: Per-extension API that writes registrations to Extension and delegates actions to runtime
 4. **ExtensionRunner**: Orchestrates event dispatch and provides context to handlers
@@ -316,7 +413,7 @@ Key extension events:
 - `user_bash`: Intercept `!`/`!!` commands for custom execution (e.g., remote SSH)
 - `session_shutdown`: Cleanup notification before exit

-### Custom Tools (core/custom-tools/)
+### Custom Tools (extensibility/custom-tools/)

 System for adding LLM-callable tools:

@@ -325,7 +422,7 @@ System for adding LLM-callable tools:

 See [docs/custom-tools.md](docs/custom-tools.md) for full documentation.

-### Skills (core/skills.ts)
+### Skills (extensibility/skills.ts)

 On-demand capability packages:

@@ -412,15 +509,15 @@ Tools like `fd` and `rg` are auto-downloaded to `~/.omp/bin/` (migrated from `~/

 ### Adding a New Tool

-1. Create tool factory in `core/tools/` following existing patterns (e.g., `createMyTool(session: ToolSession)`)
-2. Export factory and types from `core/tools/index.ts`
-3. Add to `BUILTIN_TOOLS` map in `core/tools/index.ts`
+1. Create tool factory in `tools/` following existing patterns (e.g., `createMyTool(session: ToolSession)`)
+2. Export factory and types from `tools/index.ts`
+3. Add to `BUILTIN_TOOLS` map in `tools/index.ts`
 4. Add tool prompt template to `prompts/tools/` if needed
 5. Tool will automatically be included in system prompt

 ### Adding a New Hook Event

-1. Add event type to hook event types in `core/hooks/types.ts`
+1. Add event type to hook event types in `extensibility/hooks/types.ts`
 2. Add emission point in relevant code (AgentSession, tool wrapper, etc.)
 3. Update `docs/hooks.md` with the new event type

@@ -434,7 +531,7 @@ Tools like `fd` and `rg` are auto-downloaded to `~/.omp/bin/` (migrated from `~/

 ### Adding a New Selector

-1. Create component in `modes/interactive/components/`
+1. Create component in `modes/components/`
 2. Use `showSelector()` helper in `interactive-mode.ts`:

 ```typescript
@@ -474,7 +571,7 @@ private showMySelector(): void {

 ### Adding a New Keybinding

-1. Add the action name to `AppAction` type in `core/keybindings.ts`
+1. Add the action name to `AppAction` type in `config/keybindings.ts`
 2. Add default binding to `DEFAULT_APP_KEYBINDINGS`
 3. Add to `APP_ACTIONS` array
 4. Handle the action in `CustomEditor` or `InteractiveMode`
@@ -5,7 +5,7 @@
 import type { ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import chalk from "chalk";
 import { APP_NAME, CONFIG_DIR_NAME, ENV_AGENT_DIR } from "$c/config";
-import { BUILTIN_TOOLS } from "$c/core/tools/index";
+import { BUILTIN_TOOLS } from "$c/tools/index";

 export type Mode = "text" | "json" | "rpc";

@@ -7,9 +7,9 @@

 import chalk from "chalk";
 import { APP_NAME, getAgentDir } from "$c/config";
-import { SettingsManager } from "$c/core/settings-manager";
-import { SETTINGS_DEFS, type SettingDef } from "$c/modes/interactive/components/settings-defs";
-import { theme } from "$c/modes/interactive/theme/theme";
+import { SettingsManager } from "$c/config/settings-manager";
+import { SETTINGS_DEFS, type SettingDef } from "$c/modes/components/settings-defs";
+import { theme } from "$c/modes/theme/theme";

 // =============================================================================
 // Types
@@ -6,7 +6,7 @@ import { existsSync, readFileSync, statSync } from "node:fs";
 import { resolve } from "node:path";
 import type { ImageContent } from "@oh-my-pi/pi-ai";
 import chalk from "chalk";
-import { resolveReadPath } from "$c/core/tools/path-utils";
+import { resolveReadPath } from "$c/tools/path-utils";
 import { formatDimensionNote, resizeImage } from "$c/utils/image-resize";
 import { detectSupportedImageMimeTypeFromFile } from "$c/utils/mime";

@@ -3,7 +3,7 @@
 */

 import type { Api, Model } from "@oh-my-pi/pi-ai";
-import type { ModelRegistry } from "$c/core/model-registry";
+import type { ModelRegistry } from "$c/config/model-registry";
 import { fuzzyFilter } from "$c/utils/fuzzy";

 /**
@@ -6,8 +6,8 @@

 import chalk from "chalk";
 import { APP_NAME } from "$c/config";
-import { PluginManager, parseSettingValue, validateSetting } from "$c/core/plugins/index";
-import { theme } from "$c/modes/interactive/theme/theme";
+import { PluginManager, parseSettingValue, validateSetting } from "$c/extensibility/plugins/index";
+import { theme } from "$c/modes/theme/theme";

 // =============================================================================
 // Types
@@ -3,8 +3,8 @@
 */

 import { ProcessTerminal, TUI } from "@oh-my-pi/pi-tui";
-import type { SessionInfo } from "$c/core/session-manager";
-import { SessionSelectorComponent } from "$c/modes/interactive/components/session-selector";
+import { SessionSelectorComponent } from "$c/modes/components/session-selector";
+import type { SessionInfo } from "$c/session/session-manager";

 /** Show TUI session selector and return selected session path or null if cancelled */
 export async function selectSession(sessions: SessionInfo[]): Promise<string | null> {
@@ -7,7 +7,7 @@
 import { $ } from "bun";
 import chalk from "chalk";
 import { APP_NAME } from "$c/config";
-import { theme } from "$c/modes/interactive/theme/theme";
+import { theme } from "$c/modes/theme/theme";

 export type SetupComponent = "python";

@@ -12,7 +12,7 @@ import { Readable } from "node:stream";
 import { pipeline } from "node:stream/promises";
 import chalk from "chalk";
 import { APP_NAME, VERSION } from "$c/config";
-import { theme } from "$c/modes/interactive/theme/theme";
+import { theme } from "$c/modes/theme/theme";

 /**
 * Detect if we're running as a Bun compiled binary.
@@ -14,7 +14,7 @@ import {
 import { logger } from "@oh-my-pi/pi-utils";
 import { type Static, Type } from "@sinclair/typebox";
 import AjvModule from "ajv";
-import type { AuthStorage } from "./auth-storage";
+import type { AuthStorage } from "$c/session/auth-storage";

 const Ajv = (AjvModule as any).default || AjvModule;

@@ -2,7 +2,7 @@ import { join, resolve } from "node:path";
 import { logger } from "@oh-my-pi/pi-utils";
 import Handlebars from "handlebars";
 import { CONFIG_DIR_NAME, getPromptsDir } from "$c/config";
-import { parseFrontmatter } from "./frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";

 /**
 * Represents a prompt template loaded from a markdown file
@@ -4,8 +4,8 @@ import { logger } from "@oh-my-pi/pi-utils";
 import { type Settings as SettingsItem, settingsCapability } from "$c/capability/settings";
 import { getAgentDbPath, getAgentDir } from "$c/config";
 import { loadCapability } from "$c/discovery";
-import type { SymbolPreset } from "$c/modes/interactive/theme/theme";
-import { AgentStorage } from "./agent-storage";
+import type { SymbolPreset } from "$c/modes/theme/theme";
+import { AgentStorage } from "$c/session/agent-storage";

 export interface CompactionSettings {
 	enabled?: boolean; // default: true
@@ -1,71 +0,0 @@
-/**
- * Core modules shared between all run modes.
- */
-
-export {
-	AgentSession,
-	type AgentSessionConfig,
-	type AgentSessionEvent,
-	type AgentSessionEventListener,
-	type ModelCycleResult,
-	type PromptOptions,
-	type SessionStats,
-} from "./agent-session";
-export { ArtifactManager } from "./artifacts";
-export { type BashExecutorOptions, type BashResult, executeBash } from "./bash-executor";
-export type { CompactionResult } from "./compaction/index";
-export {
-	discoverAndLoadExtensions,
-	type ExtensionAPI,
-	type ExtensionCommandContext,
-	type ExtensionContext,
-	type ExtensionFactory,
-	ExtensionRunner,
-	type ExtensionUIContext,
-	type ExtensionUIDialogOptions,
-	loadExtensionFromFactory,
-	type ToolDefinition,
-} from "./extensions/index";
-export { HistoryStorage } from "./history-storage";
-export {
-	createMCPManager,
-	discoverAndLoadMCPTools,
-	loadAllMCPConfigs,
-	type MCPConfigFile,
-	type MCPLoadResult,
-	MCPManager,
-	type MCPServerConfig,
-	type MCPServerConnection,
-	MCPToolCache,
-	type MCPToolDefinition,
-	type MCPToolDetails,
-	type MCPToolsLoadResult,
-	type MCPTransport,
-} from "./mcp/index";
-export {
-	type DiagnosticMeta,
-	type LimitsMeta,
-	type OutputMeta,
-	OutputMetaBuilder,
-	outputMeta,
-	type SourceMeta,
-	type TruncationMeta,
-	type TruncationOptions,
-	wrapToolsWithMetaNotice,
-	wrapToolWithMetaNotice,
-} from "./output-meta";
-export {
-	buildRemoteCommand,
-	closeAllConnections,
-	closeConnection,
-	ensureConnection,
-	getControlDir,
-	getControlPathTemplate,
-	type SSHConnectionTarget,
-} from "./ssh/connection-manager";
-export { executeSSH, type SSHExecutorOptions, type SSHResult } from "./ssh/ssh-executor";
-export { hasSshfs, isMounted, mountRemote, unmountAll, unmountRemote } from "./ssh/sshfs-mount";
-export { OutputSink, type OutputSinkOptions, type OutputSummary } from "./streaming-output";
-export { type ErrorEntry, MultiError, renderError, ToolError } from "./tool-errors";
-
-export * as utils from "./utils";
@@ -1,3 +0,0 @@
-import pythonPrelude from "./python-prelude.py" with { type: "text" };
-
-export const PYTHON_PRELUDE = pythonPrelude;
@@ -1,5 +0,0 @@
-/**
- * Backwards-compatible re-export for SSH execution.
- */
-
-export { executeSSH, type SSHExecutorOptions, type SSHResult } from "./ssh/ssh-executor";
@@ -8,7 +8,7 @@ import type {
 	AgentToolUpdateCallback,
 } from "@oh-my-pi/pi-agent-core";
 import type { CursorMcpCall, CursorExecHandlers as ICursorExecHandlers, ToolResultMessage } from "@oh-my-pi/pi-ai";
-import { resolveToCwd } from "$c/core/tools/path-utils";
+import { resolveToCwd } from "$c/tools/path-utils";

 interface CursorExecBridgeOptions {
 	cwd: string;
@@ -22,7 +22,7 @@ import { type SlashCommand, slashCommandCapability } from "$c/capability/slash-c
 import { type SystemPrompt, systemPromptCapability } from "$c/capability/system-prompt";
 import { type CustomTool, toolCapability } from "$c/capability/tool";
 import type { LoadContext, LoadResult } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";
 import {
 	createSourceMeta,
 	discoverExtensionModulePaths,
@@ -11,7 +11,7 @@ import { registerProvider } from "$c/capability/index";
 import type { Rule } from "$c/capability/rule";
 import { ruleCapability } from "$c/capability/rule";
 import type { LoadContext, LoadResult } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";
 import { createSourceMeta, loadFilesFromDir } from "./helpers";

 const PROVIDER_ID = "cline";
@@ -30,7 +30,7 @@ import { slashCommandCapability } from "$c/capability/slash-command";
 import type { CustomTool } from "$c/capability/tool";
 import { toolCapability } from "$c/capability/tool";
 import type { LoadContext, LoadResult } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";
 import {
 	createSourceMeta,
 	discoverExtensionModulePaths,
@@ -22,7 +22,7 @@ import { ruleCapability } from "$c/capability/rule";
 import type { Settings } from "$c/capability/settings";
 import { settingsCapability } from "$c/capability/settings";
 import type { LoadContext, LoadResult } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";
 import {
 	createSourceMeta,
 	expandEnvVarsDeep,
@@ -18,7 +18,7 @@ import { readFile } from "$c/capability/fs";
 import { registerProvider } from "$c/capability/index";
 import { type Instruction, instructionCapability } from "$c/capability/instruction";
 import type { LoadContext, LoadResult, SourceMeta } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";
 import { calculateDepth, createSourceMeta, getProjectPath, loadFilesFromDir } from "./helpers";

 const PROVIDER_ID = "github";
@@ -8,7 +8,7 @@ import type { ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import { readDirEntries, readFile } from "$c/capability/fs";
 import type { Skill, SkillFrontmatter } from "$c/capability/skill";
 import type { LoadContext, LoadResult, SourceMeta } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";

 const VALID_THINKING_LEVELS: readonly string[] = ["off", "minimal", "low", "medium", "high", "xhigh"];
 const UNICODE_SPACES = /[\u00A0\u2000-\u200A\u202F\u205F\u3000]/g;
@@ -16,7 +16,7 @@ import { registerProvider } from "$c/capability/index";
 import { type MCPServer, mcpCapability } from "$c/capability/mcp";
 import { type Rule, ruleCapability } from "$c/capability/rule";
 import type { LoadContext, LoadResult } from "$c/capability/types";
-import { parseFrontmatter } from "$c/core/frontmatter";
+import { parseFrontmatter } from "$c/utils/frontmatter";
 import {
 	createSourceMeta,
 	expandEnvVarsDeep,
@@ -5,7 +5,7 @@
 */

 import { Type } from "@sinclair/typebox";
-import type { CustomTool } from "$c/core/custom-tools/types";
+import type { CustomTool } from "$c/extensibility/custom-tools/types";
 import { callExaTool, findApiKey, formatSearchResults, isSearchResponse } from "./mcp-client";
 import type { ExaRenderDetails } from "./types";

@@ -9,8 +9,8 @@
 * - 14 websets tools (CRUD, items, search, enrichment, monitor)
 */

-import type { CustomTool } from "$c/core/custom-tools/types";
-import type { ExaSettings } from "$c/core/settings-manager";
+import type { ExaSettings } from "$c/config/settings-manager";
+import type { CustomTool } from "$c/extensibility/custom-tools/types";
 import { companyTool } from "./company";
 import { linkedinTool } from "./linkedin";
 import { researcherTools } from "./researcher";
@@ -5,7 +5,7 @@
 */

 import { Type } from "@sinclair/typebox";
-import type { CustomTool } from "$c/core/custom-tools/types";
+import type { CustomTool } from "$c/extensibility/custom-tools/types";
 import { callExaTool, findApiKey, formatSearchResults, isSearchResponse } from "./mcp-client";
 import type { ExaRenderDetails } from "./types";

@@ -8,8 +8,8 @@ import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { logger } from "@oh-my-pi/pi-utils";
 import type { TSchema } from "@sinclair/typebox";
-import type { CustomTool, CustomToolResult } from "$c/core/custom-tools/types";
-import { callMCP } from "$c/core/mcp/json-rpc";
+import type { CustomTool, CustomToolResult } from "$c/extensibility/custom-tools/types";
+import { callMCP } from "$c/mcp/json-rpc";
 import type {
 	ExaRenderDetails,
 	ExaSearchResponse,
@@ -7,7 +7,8 @@
 import type { Component } from "@oh-my-pi/pi-tui";
 import { Text } from "@oh-my-pi/pi-tui";
 import { logger } from "@oh-my-pi/pi-utils";
-import type { RenderResultOptions } from "$c/core/custom-tools/types";
+import type { RenderResultOptions } from "$c/extensibility/custom-tools/types";
+import type { Theme } from "$c/modes/theme/theme";
 import {
 	formatCount,
 	formatExpandHint,
@@ -18,8 +19,7 @@ import {
 	PREVIEW_LIMITS,
 	TRUNCATE_LENGTHS,
 	truncate,
-} from "$c/core/tools/render-utils";
-import type { Theme } from "$c/modes/interactive/theme/theme";
+} from "$c/tools/render-utils";
 import type { ExaRenderDetails } from "./types";

 const COLLAPSED_PREVIEW_LINES = PREVIEW_LIMITS.COLLAPSED_LINES;
@@ -5,7 +5,7 @@
 */

 import { Type } from "@sinclair/typebox";
-import type { CustomTool } from "$c/core/custom-tools/types";
+import type { CustomTool } from "$c/extensibility/custom-tools/types";
 import { callExaTool, findApiKey } from "./mcp-client";
 import type { ExaRenderDetails } from "./types";

@@ -6,7 +6,7 @@

 import { StringEnum } from "@oh-my-pi/pi-ai";
 import { Type } from "@sinclair/typebox";
-import type { CustomTool } from "$c/core/custom-tools/types";
+import type { CustomTool } from "$c/extensibility/custom-tools/types";
 import { callExaTool, findApiKey, formatSearchResults, isSearchResponse } from "./mcp-client";
 import type { ExaRenderDetails } from "./types";

@@ -5,7 +5,7 @@
 */

 import { Type } from "@sinclair/typebox";
-import type { CustomTool } from "$c/core/custom-tools/types";
+import type { CustomTool } from "$c/extensibility/custom-tools/types";
 import { callWebsetsTool, findApiKey } from "./mcp-client";
 import type { ExaRenderDetails } from "./types";

@@ -5,9 +5,9 @@
 */

 import { cspawn, Exception, ptree } from "@oh-my-pi/pi-utils";
+import { OutputSink } from "$c/session/streaming-output";
 import { getShellConfig } from "$c/utils/shell";
 import { getOrCreateSnapshot, getSnapshotSourceCommand } from "$c/utils/shell-snapshot";
-import { OutputSink } from "./streaming-output";

 export interface BashExecutorOptions {
 	cwd?: string;
@@ -2,8 +2,8 @@ import { existsSync, writeFileSync } from "node:fs";
 import { basename } from "node:path";
 import type { AgentState } from "@oh-my-pi/pi-agent-core";
 import { APP_NAME } from "$c/config";
-import { SessionManager } from "$c/core/session-manager";
-import { getResolvedThemeColors, getThemeExportColors } from "$c/modes/interactive/theme/theme";
+import { getResolvedThemeColors, getThemeExportColors } from "$c/modes/theme/theme";
+import { SessionManager } from "$c/session/session-manager";

 // Pre-generated template (created by scripts/generate-template.ts at publish time)
 import { TEMPLATE } from "./template.generated";
@@ -8,7 +8,7 @@

 import { logger } from "@oh-my-pi/pi-utils";
 import type { Rule } from "$c/capability/rule";
-import type { TtsrSettings } from "./settings-manager";
+import type { TtsrSettings } from "$c/config/settings-manager";

 interface TtsrEntry {
 	rule: Rule;
@@ -12,9 +12,9 @@
 * multiple reviewer agents based on diff weight and locality.
 */

-import type { CustomCommand, CustomCommandAPI } from "$c/core/custom-commands/types";
-import type { HookCommandContext } from "$c/core/hooks/types";
-import { renderPromptTemplate } from "$c/core/prompt-templates";
+import { renderPromptTemplate } from "$c/config/prompt-templates";
+import type { CustomCommand, CustomCommandAPI } from "$c/extensibility/custom-commands/types";
+import type { HookCommandContext } from "$c/extensibility/hooks/types";
 import reviewRequestTemplate from "$c/prompts/review-request.md" with { type: "text" };

 // ─────────────────────────────────────────────────────────────────────────────
@@ -10,7 +10,7 @@ import * as path from "node:path";
 import { logger } from "@oh-my-pi/pi-utils";
 import * as typebox from "@sinclair/typebox";
 import { getAgentDir, getConfigDirs } from "$c/config";
-import { execCommand } from "$c/core/exec";
+import { execCommand } from "$c/exec/exec";
 import * as piCodingAgent from "$c/index";
 import { ReviewCommand } from "./bundled/review";
 import type {
@@ -6,7 +6,7 @@
 * arbitrary logic with full access to the hook context.
 */

-import type { ExecOptions, ExecResult, HookCommandContext } from "$c/core/hooks/types";
+import type { ExecOptions, ExecResult, HookCommandContext } from "$c/extensibility/hooks/types";

 // Re-export for custom commands to use
 export type { ExecOptions, ExecResult, HookCommandContext };
@@ -9,14 +9,14 @@ import * as path from "node:path";
 import { logger } from "@oh-my-pi/pi-utils";
 import * as typebox from "@sinclair/typebox";
 import { toolCapability } from "$c/capability/tool";
-import type { ExecOptions } from "$c/core/exec";
-import { execCommand } from "$c/core/exec";
-import type { HookUIContext } from "$c/core/hooks/types";
-import { getAllPluginToolPaths } from "$c/core/plugins/loader";
 import { type CustomTool, loadCapability } from "$c/discovery";
 import { expandPath } from "$c/discovery/helpers";
+import type { ExecOptions } from "$c/exec/exec";
+import { execCommand } from "$c/exec/exec";
+import type { HookUIContext } from "$c/extensibility/hooks/types";
+import { getAllPluginToolPaths } from "$c/extensibility/plugins/loader";
 import * as piCodingAgent from "$c/index";
-import { theme } from "$c/modes/interactive/theme/theme";
+import { theme } from "$c/modes/theme/theme";
 import type { CustomToolAPI, CustomToolFactory, LoadedCustomTool, ToolLoadError } from "./types";

 /**
@@ -9,11 +9,11 @@ import type { AgentToolResult, AgentToolUpdateCallback } from "@oh-my-pi/pi-agen
 import type { Model } from "@oh-my-pi/pi-ai";
 import type { Component } from "@oh-my-pi/pi-tui";
 import type { Static, TSchema } from "@sinclair/typebox";
-import type { ExecOptions, ExecResult } from "$c/core/exec";
-import type { HookUIContext } from "$c/core/hooks/types";
-import type { ModelRegistry } from "$c/core/model-registry";
-import type { ReadonlySessionManager } from "$c/core/session-manager";
-import type { Theme } from "$c/modes/interactive/theme/theme";
+import type { ModelRegistry } from "$c/config/model-registry";
+import type { ExecOptions, ExecResult } from "$c/exec/exec";
+import type { HookUIContext } from "$c/extensibility/hooks/types";
+import type { Theme } from "$c/modes/theme/theme";
+import type { ReadonlySessionManager } from "$c/session/session-manager";

 /** Alias for clarity */
 export type CustomToolUIContext = HookUIContext;
@@ -22,7 +22,7 @@ export type CustomToolUIContext = HookUIContext;
 export type { AgentToolResult, AgentToolUpdateCallback };

 // Re-export for backward compatibility
-export type { ExecOptions, ExecResult } from "$c/core/exec";
+export type { ExecOptions, ExecResult } from "$c/exec/exec";

 /** API passed to custom tool factory (stable across session changes) */
 export interface CustomToolAPI {
@@ -5,7 +5,7 @@
 import type { AgentTool, AgentToolResult, AgentToolUpdateCallback, RenderResultOptions } from "@oh-my-pi/pi-agent-core";
 import type { Component } from "@oh-my-pi/pi-tui";
 import type { Static, TSchema } from "@sinclair/typebox";
-import type { Theme } from "$c/modes/interactive/theme/theme";
+import type { Theme } from "$c/modes/theme/theme";
 import type { CustomTool, CustomToolContext, LoadedCustomTool } from "./types";

 export class CustomToolAdapter<TParams extends TSchema = TSchema, TDetails = any, TTheme extends Theme = Theme>
@@ -11,13 +11,13 @@ import { logger } from "@oh-my-pi/pi-utils";
 import type { TSchema } from "@sinclair/typebox";
 import * as TypeBox from "@sinclair/typebox";
 import { type ExtensionModule, extensionModuleCapability } from "$c/capability/extension-module";
-import { EventBus } from "$c/core/event-bus";
-import type { ExecOptions } from "$c/core/exec";
-import { execCommand } from "$c/core/exec";
-import type { CustomMessage } from "$c/core/messages";
 import { loadCapability } from "$c/discovery";
 import { expandPath, getExtensionNameFromPath } from "$c/discovery/helpers";
+import type { ExecOptions } from "$c/exec/exec";
+import { execCommand } from "$c/exec/exec";
 import * as piCodingAgent from "$c/index";
+import type { CustomMessage } from "$c/session/messages";
+import { EventBus } from "$c/utils/event-bus";
 import type {
 	Extension,
 	ExtensionAPI,
@@ -6,9 +6,9 @@ import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
 import type { ImageContent, Model } from "@oh-my-pi/pi-ai";
 import type { KeyId } from "@oh-my-pi/pi-tui";
 import { logger } from "@oh-my-pi/pi-utils";
-import type { ModelRegistry } from "$c/core/model-registry";
-import type { SessionManager } from "$c/core/session-manager";
-import { type Theme, theme } from "$c/modes/interactive/theme/theme";
+import type { ModelRegistry } from "$c/config/model-registry";
+import { type Theme, theme } from "$c/modes/theme/theme";
+import type { SessionManager } from "$c/session/session-manager";
 import type {
 	BeforeAgentStartEvent,
 	BeforeAgentStartEventResult,
@@ -12,28 +12,28 @@ import type { AgentMessage, AgentToolResult, AgentToolUpdateCallback, ThinkingLe
 import type { ImageContent, Model, TextContent, ToolResultMessage } from "@oh-my-pi/pi-ai";
 import type { AutocompleteItem, Component, EditorComponent, EditorTheme, KeyId, TUI } from "@oh-my-pi/pi-tui";
 import type { Static, TSchema } from "@sinclair/typebox";
-import type { BashResult } from "$c/core/bash-executor";
-import type { CompactionPreparation, CompactionResult } from "$c/core/compaction";
-import type { EventBus } from "$c/core/event-bus";
-import type { ExecOptions, ExecResult } from "$c/core/exec";
-import type { KeybindingsManager } from "$c/core/keybindings";
-import type { CustomMessage } from "$c/core/messages";
-import type { ModelRegistry } from "$c/core/model-registry";
-import type { PythonResult } from "$c/core/python-executor";
+import type { KeybindingsManager } from "$c/config/keybindings";
+import type { ModelRegistry } from "$c/config/model-registry";
+import type { BashResult } from "$c/exec/bash-executor";
+import type { ExecOptions, ExecResult } from "$c/exec/exec";
+import type * as piCodingAgent from "$c/index";
+import type { PythonResult } from "$c/ipy/executor";
+import type { Theme } from "$c/modes/theme/theme";
+import type { EditToolDetails } from "$c/patch";
+import type { CompactionPreparation, CompactionResult } from "$c/session/compaction";
+import type { CustomMessage } from "$c/session/messages";
 import type {
 	BranchSummaryEntry,
 	CompactionEntry,
 	ReadonlySessionManager,
 	SessionEntry,
 	SessionManager,
-} from "$c/core/session-manager";
-import type { BashToolDetails, FindToolDetails, GrepToolDetails, LsToolDetails, ReadToolDetails } from "$c/core/tools";
-import type { EditToolDetails } from "$c/core/tools/patch";
-import type * as piCodingAgent from "$c/index";
-import type { Theme } from "$c/modes/interactive/theme/theme";
+} from "$c/session/session-manager";
+import type { BashToolDetails, FindToolDetails, GrepToolDetails, LsToolDetails, ReadToolDetails } from "$c/tools";
+import type { EventBus } from "$c/utils/event-bus";

-export type { ExecOptions, ExecResult } from "$c/core/exec";
-export type { AppAction, KeybindingsManager } from "$c/core/keybindings";
+export type { AppAction, KeybindingsManager } from "$c/config/keybindings";
+export type { ExecOptions, ExecResult } from "$c/exec/exec";
 export type { AgentToolResult, AgentToolUpdateCallback };

 // ============================================================================
@@ -5,7 +5,7 @@
 import type { AgentTool, AgentToolContext, AgentToolUpdateCallback } from "@oh-my-pi/pi-agent-core";
 import type { ImageContent, TextContent } from "@oh-my-pi/pi-ai";
 import type { Static, TSchema } from "@sinclair/typebox";
-import type { Theme } from "$c/modes/interactive/theme/theme";
+import type { Theme } from "$c/modes/theme/theme";
 import type { ExtensionRunner } from "./runner";
 import type { RegisteredTool, ToolCallEventResult, ToolResultEventResult } from "./types";

@@ -1,5 +1,5 @@
 // biome-ignore assist/source/organizeImports: biome is not smart
-export type { ReadonlySessionManager, UsageStatistics } from "$c/core/session-manager";
+export type { ReadonlySessionManager, UsageStatistics } from "$c/session/session-manager";
 export {
 	discoverAndLoadHooks,
 	loadHooks,
@@ -6,12 +6,12 @@ import * as path from "node:path";
 import { logger } from "@oh-my-pi/pi-utils";
 import * as typebox from "@sinclair/typebox";
 import { hookCapability } from "$c/capability/hook";
-import type { HookMessage } from "$c/core/messages";
-import type { SessionManager } from "$c/core/session-manager";
 import type { Hook } from "$c/discovery";
 import { loadCapability } from "$c/discovery";
 import { expandPath } from "$c/discovery/helpers";
 import * as piCodingAgent from "$c/index";
+import type { HookMessage } from "$c/session/messages";
+import type { SessionManager } from "$c/session/session-manager";
 import { execCommand } from "./runner";
 import type { ExecOptions, HookAPI, HookFactory, HookMessageRenderer, RegisteredCommand } from "./types";

@@ -4,9 +4,9 @@

 import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
 import type { Model } from "@oh-my-pi/pi-ai";
-import type { ModelRegistry } from "$c/core/model-registry";
-import type { SessionManager } from "$c/core/session-manager";
-import { theme } from "$c/modes/interactive/theme/theme";
+import type { ModelRegistry } from "$c/config/model-registry";
+import { theme } from "$c/modes/theme/theme";
+import type { SessionManager } from "$c/session/session-manager";
 import type {
 	AppendEntryHandler,
 	BranchHandler,
@@ -40,7 +40,7 @@ import type {
 export type HookErrorListener = (error: HookError) => void;

 // Re-export execCommand for backward compatibility
-export { execCommand } from "$c/core/exec";
+export { execCommand } from "$c/exec/exec";

 /** No-op UI context used when no UI is available */
 const noOpUIContext: HookUIContext = {
@@ -8,29 +8,23 @@
 import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
 import type { ImageContent, Message, Model, TextContent, ToolResultMessage } from "@oh-my-pi/pi-ai";
 import type { Component, TUI } from "@oh-my-pi/pi-tui";
-import type { CompactionPreparation, CompactionResult } from "$c/core/compaction/index";
-import type { ExecOptions, ExecResult } from "$c/core/exec";
-import type { HookMessage } from "$c/core/messages";
-import type { ModelRegistry } from "$c/core/model-registry";
+import type { ModelRegistry } from "$c/config/model-registry";
+import type { ExecOptions, ExecResult } from "$c/exec/exec";
+import type { Theme } from "$c/modes/theme/theme";
+import type { EditToolDetails } from "$c/patch";
+import type { CompactionPreparation, CompactionResult } from "$c/session/compaction/index";
+import type { HookMessage } from "$c/session/messages";
 import type {
 	BranchSummaryEntry,
 	CompactionEntry,
 	ReadonlySessionManager,
 	SessionEntry,
 	SessionManager,
-} from "$c/core/session-manager";
-import type {
-	BashToolDetails,
-	FindToolDetails,
-	GrepToolDetails,
-	LsToolDetails,
-	ReadToolDetails,
-} from "$c/core/tools/index";
-import type { EditToolDetails } from "$c/core/tools/patch";
-import type { Theme } from "$c/modes/interactive/theme/theme";
+} from "$c/session/session-manager";
+import type { BashToolDetails, FindToolDetails, GrepToolDetails, LsToolDetails, ReadToolDetails } from "$c/tools/index";

 // Re-export for backward compatibility
-export type { ExecOptions, ExecResult } from "$c/core/exec";
+export type { ExecOptions, ExecResult } from "$c/exec/exec";

 /**
 * UI context for hooks to request interactive UI from the harness.
@@ -1,4 +1,4 @@
-import { theme } from "$c/modes/interactive/theme/theme";
+import { theme } from "$c/modes/theme/theme";
 import type { DoctorCheck } from "./types";

 export async function runDoctorChecks(): Promise<DoctorCheck[]> {
@@ -4,10 +4,10 @@ import { basename, join } from "node:path";
 import { logger } from "@oh-my-pi/pi-utils";
 import { skillCapability } from "$c/capability/skill";
 import type { SourceMeta } from "$c/capability/types";
+import type { SkillsSettings } from "$c/config/settings-manager";
 import type { Skill as CapabilitySkill, SkillFrontmatter as ImportedSkillFrontmatter } from "$c/discovery";
 import { loadCapability } from "$c/discovery";
-import { parseFrontmatter } from "./frontmatter";
-import type { SkillsSettings } from "./settings-manager";
+import { parseFrontmatter } from "$c/utils/frontmatter";

 // Re-export SkillFrontmatter for backward compatibility
 export type { ImportedSkillFrontmatter as SkillFrontmatter };
@@ -1,9 +1,9 @@
 import { slashCommandCapability } from "$c/capability/slash-command";
+import { renderPromptTemplate } from "$c/config/prompt-templates";
 import type { SlashCommand } from "$c/discovery";
 import { loadCapability } from "$c/discovery";
-import { parseFrontmatter } from "./frontmatter";
-import { renderPromptTemplate } from "./prompt-templates";
-import { EMBEDDED_COMMAND_TEMPLATES } from "./tools/task/commands";
+import { EMBEDDED_COMMAND_TEMPLATES } from "$c/task/commands";
+import { parseFrontmatter } from "$c/utils/frontmatter";

 /**
 * Represents a custom slash command loaded from a file
@@ -7,230 +7,7 @@ export { StringEnum } from "@oh-my-pi/pi-ai";
 export { Container, Markdown, Spacer, Text } from "@oh-my-pi/pi-tui";
 // Logging
 export { logger } from "@oh-my-pi/pi-utils";
-export { getAgentDir, VERSION } from "./config";
-export {
-	AgentSession,
-	type AgentSessionConfig,
-	type AgentSessionEvent,
-	type AgentSessionEventListener,
-	type ModelCycleResult,
-	type PromptOptions,
-	type SessionStats,
-} from "./core/agent-session";
-// Auth and model registry
-export { type ApiKeyCredential, type AuthCredential, AuthStorage, type OAuthCredential } from "./core/auth-storage";
-// Compaction
-export {
-	type BranchPreparation,
-	type BranchSummaryResult,
-	type CollectEntriesResult,
-	type CompactionResult,
-	type CutPointResult,
-	calculateContextTokens,
-	collectEntriesForBranchSummary,
-	compact,
-	DEFAULT_COMPACTION_SETTINGS,
-	estimateTokens,
-	type FileOperations,
-	findCutPoint,
-	findTurnStartIndex,
-	type GenerateBranchSummaryOptions,
-	generateBranchSummary,
-	generateSummary,
-	getLastAssistantUsage,
-	prepareBranchEntries,
-	serializeConversation,
-	shouldCompact,
-} from "./core/compaction/index";
-// Custom commands
-export type {
-	CustomCommand,
-	CustomCommandAPI,
-	CustomCommandFactory,
-	CustomCommandSource,
-	CustomCommandsLoadResult,
-	LoadedCustomCommand,
-} from "./core/custom-commands/types";
-export type {
-	AgentToolUpdateCallback,
-	CustomTool,
-	CustomToolAPI,
-	CustomToolContext,
-	CustomToolFactory,
-	CustomToolSessionEvent,
-	CustomToolsLoadResult,
-	CustomToolUIContext,
-	ExecResult,
-	LoadedCustomTool,
-	RenderResultOptions,
-} from "./core/custom-tools/index";
-// Custom tools
-export { CustomToolLoader, discoverAndLoadCustomTools, loadCustomTools } from "./core/custom-tools/index";
-export type {
-	AppAction,
-	Extension,
-	ExtensionActions,
-	ExtensionAPI,
-	ExtensionCommandContext,
-	ExtensionCommandContextActions,
-	ExtensionContext,
-	ExtensionContextActions,
-	ExtensionError,
-	ExtensionEvent,
-	ExtensionFactory,
-	ExtensionFlag,
-	ExtensionHandler,
-	ExtensionShortcut,
-	ExtensionUIContext,
-	ExtensionUIDialogOptions,
-	InputEvent,
-	InputEventResult,
-	KeybindingsManager,
-	LoadExtensionsResult,
-	MessageRenderer,
-	MessageRenderOptions,
-	RegisteredCommand,
-	ToolResultEvent,
-	TurnEndEvent,
-	TurnStartEvent,
-	UserBashEvent,
-	UserBashEventResult,
-	UserPythonEvent,
-	UserPythonEventResult,
-} from "./core/extensions/index";
-// Extension types and utilities
-export {
-	discoverAndLoadExtensions,
-	ExtensionRunner,
-	ExtensionRuntime,
-	isBashToolResult,
-	isEditToolResult,
-	isFindToolResult,
-	isGrepToolResult,
-	isLsToolResult,
-	isReadToolResult,
-	isWriteToolResult,
-} from "./core/extensions/index";
-// Hook system types (legacy re-export)
-export type * from "./core/hooks/index";
-export { formatKeyHint, formatKeyHints } from "./core/keybindings";
-export { convertToLlm } from "./core/messages";
-export { ModelRegistry } from "./core/model-registry";
-// Prompt templates
-export type { PromptTemplate } from "./core/prompt-templates";
-// SDK for programmatic usage
-export {
-	// Factory
-	BashTool,
-	// Tool factories
-	BUILTIN_TOOLS,
-	type BuildSystemPromptOptions,
-	buildSystemPrompt,
-	type CreateAgentSessionOptions,
-	type CreateAgentSessionResult,
-	createAgentSession,
-	createTools,
-	// Discovery
-	discoverAuthStorage,
-	discoverContextFiles,
-	discoverCustomTSCommands,
-	discoverExtensions,
-	discoverMCPServers,
-	discoverModels,
-	discoverPromptTemplates,
-	discoverSkills,
-	EditTool,
-	FindTool,
-	GrepTool,
-	LsTool,
-	loadSettings,
-	loadSshTool,
-	PythonTool,
-	ReadTool,
-	type ToolSession,
-	WriteTool,
-} from "./core/sdk";
-export {
-	type BranchSummaryEntry,
-	buildSessionContext,
-	type CompactionEntry,
-	CURRENT_SESSION_VERSION,
-	type CustomEntry,
-	type CustomMessageEntry,
-	type FileEntry,
-	getLatestCompactionEntry,
-	type ModelChangeEntry,
-	migrateSessionEntries,
-	type NewSessionOptions,
-	parseSessionEntries,
-	type SessionContext,
-	type SessionEntry,
-	type SessionEntryBase,
-	type SessionHeader,
-	type SessionInfo,
-	SessionManager,
-	type SessionMessageEntry,
-	type ThinkingLevelChangeEntry,
-} from "./core/session-manager";
-export {
-	type CompactionSettings,
-	type ImageSettings,
-	type LspSettings,
-	type RetrySettings,
-	type Settings,
-	SettingsManager,
-	type SkillsSettings,
-} from "./core/settings-manager";
-// Skills
-export {
-	type LoadSkillsFromDirOptions,
-	type LoadSkillsResult,
-	loadSkills,
-	loadSkillsFromDir,
-	type Skill,
-	type SkillFrontmatter,
-	type SkillWarning,
-} from "./core/skills";
-// Slash commands
-export { type FileSlashCommand, loadSlashCommands as discoverSlashCommands } from "./core/slash-commands";
-// Tools (detail types and utilities)
-export {
-	type BashToolDetails,
-	DEFAULT_MAX_BYTES,
-	DEFAULT_MAX_LINES,
-	type FindOperations,
-	type FindToolDetails,
-	type FindToolOptions,
-	formatSize,
-	type GrepOperations,
-	type GrepToolDetails,
-	type GrepToolOptions,
-	type LsOperations,
-	type LsToolDetails,
-	type LsToolOptions,
-	type PythonToolDetails,
-	type ReadToolDetails,
-	type TruncationOptions,
-	type TruncationResult,
-	truncateHead,
-	truncateLine,
-	truncateTail,
-	type WriteToolDetails,
-} from "./core/tools/index";
-export type { FileDiagnosticsResult } from "./core/tools/lsp/index";
-// Main entry point
-export { main } from "./main";
-// Run modes for programmatic SDK usage
-export {
-	InteractiveMode,
-	type InteractiveModeOptions,
-	type PrintModeOptions,
-	RpcClient,
-	type RpcClientOptions,
-	type RpcEventListener,
-	runPrintMode,
-	runRpcMode,
-} from "./modes/index";
+export type { FileDiagnosticsResult } from "$c/lsp/index";
 // UI components for extensions
 export {
 	ArminComponent,
@@ -264,7 +41,7 @@ export {
 	UserMessageComponent,
 	UserMessageSelectorComponent,
 	type VisualTruncateResult,
-} from "./modes/interactive/components/index";
+} from "$c/modes/components/index";
 // Theme utilities for custom tools
 export {
 	getLanguageFromPath,
@@ -275,5 +52,228 @@ export {
 	initTheme,
 	Theme,
 	type ThemeColor,
-} from "./modes/interactive/theme/theme";
+} from "$c/modes/theme/theme";
+export { getAgentDir, VERSION } from "./config";
+export { formatKeyHint, formatKeyHints } from "./config/keybindings";
+export { ModelRegistry } from "./config/model-registry";
+// Prompt templates
+export type { PromptTemplate } from "./config/prompt-templates";
+export {
+	type CompactionSettings,
+	type ImageSettings,
+	type LspSettings,
+	type RetrySettings,
+	type Settings,
+	SettingsManager,
+	type SkillsSettings,
+} from "./config/settings-manager";
+// Custom commands
+export type {
+	CustomCommand,
+	CustomCommandAPI,
+	CustomCommandFactory,
+	CustomCommandSource,
+	CustomCommandsLoadResult,
+	LoadedCustomCommand,
+} from "./extensibility/custom-commands/types";
+export type {
+	AgentToolUpdateCallback,
+	CustomTool,
+	CustomToolAPI,
+	CustomToolContext,
+	CustomToolFactory,
+	CustomToolSessionEvent,
+	CustomToolsLoadResult,
+	CustomToolUIContext,
+	ExecResult,
+	LoadedCustomTool,
+	RenderResultOptions,
+} from "./extensibility/custom-tools/index";
+// Custom tools
+export { CustomToolLoader, discoverAndLoadCustomTools, loadCustomTools } from "./extensibility/custom-tools/index";
+export type {
+	AppAction,
+	Extension,
+	ExtensionActions,
+	ExtensionAPI,
+	ExtensionCommandContext,
+	ExtensionCommandContextActions,
+	ExtensionContext,
+	ExtensionContextActions,
+	ExtensionError,
+	ExtensionEvent,
+	ExtensionFactory,
+	ExtensionFlag,
+	ExtensionHandler,
+	ExtensionShortcut,
+	ExtensionUIContext,
+	ExtensionUIDialogOptions,
+	InputEvent,
+	InputEventResult,
+	KeybindingsManager,
+	LoadExtensionsResult,
+	MessageRenderer,
+	MessageRenderOptions,
+	RegisteredCommand,
+	ToolResultEvent,
+	TurnEndEvent,
+	TurnStartEvent,
+	UserBashEvent,
+	UserBashEventResult,
+	UserPythonEvent,
+	UserPythonEventResult,
+} from "./extensibility/extensions/index";
+// Extension types and utilities
+export {
+	discoverAndLoadExtensions,
+	ExtensionRunner,
+	ExtensionRuntime,
+	isBashToolResult,
+	isEditToolResult,
+	isFindToolResult,
+	isGrepToolResult,
+	isLsToolResult,
+	isReadToolResult,
+	isWriteToolResult,
+} from "./extensibility/extensions/index";
+// Hook system types (legacy re-export)
+export type * from "./extensibility/hooks/index";
+// Skills
+export {
+	type LoadSkillsFromDirOptions,
+	type LoadSkillsResult,
+	loadSkills,
+	loadSkillsFromDir,
+	type Skill,
+	type SkillFrontmatter,
+	type SkillWarning,
+} from "./extensibility/skills";
+// Slash commands
+export { type FileSlashCommand, loadSlashCommands as discoverSlashCommands } from "./extensibility/slash-commands";
+// Main entry point
+export { main } from "./main";
+// Run modes for programmatic SDK usage
+export {
+	InteractiveMode,
+	type InteractiveModeOptions,
+	type PrintModeOptions,
+	RpcClient,
+	type RpcClientOptions,
+	type RpcEventListener,
+	runPrintMode,
+	runRpcMode,
+} from "./modes/index";
+// SDK for programmatic usage
+export {
+	// Factory
+	BashTool,
+	// Tool factories
+	BUILTIN_TOOLS,
+	type BuildSystemPromptOptions,
+	buildSystemPrompt,
+	type CreateAgentSessionOptions,
+	type CreateAgentSessionResult,
+	createAgentSession,
+	createTools,
+	// Discovery
+	discoverAuthStorage,
+	discoverContextFiles,
+	discoverCustomTSCommands,
+	discoverExtensions,
+	discoverMCPServers,
+	discoverModels,
+	discoverPromptTemplates,
+	discoverSkills,
+	EditTool,
+	FindTool,
+	GrepTool,
+	LsTool,
+	loadSettings,
+	loadSshTool,
+	PythonTool,
+	ReadTool,
+	type ToolSession,
+	WriteTool,
+} from "./sdk";
+export {
+	AgentSession,
+	type AgentSessionConfig,
+	type AgentSessionEvent,
+	type AgentSessionEventListener,
+	type ModelCycleResult,
+	type PromptOptions,
+	type SessionStats,
+} from "./session/agent-session";
+// Auth and model registry
+export { type ApiKeyCredential, type AuthCredential, AuthStorage, type OAuthCredential } from "./session/auth-storage";
+// Compaction
+export {
+	type BranchPreparation,
+	type BranchSummaryResult,
+	type CollectEntriesResult,
+	type CompactionResult,
+	type CutPointResult,
+	calculateContextTokens,
+	collectEntriesForBranchSummary,
+	compact,
+	DEFAULT_COMPACTION_SETTINGS,
+	estimateTokens,
+	type FileOperations,
+	findCutPoint,
+	findTurnStartIndex,
+	type GenerateBranchSummaryOptions,
+	generateBranchSummary,
+	generateSummary,
+	getLastAssistantUsage,
+	prepareBranchEntries,
+	serializeConversation,
+	shouldCompact,
+} from "./session/compaction/index";
+export { convertToLlm } from "./session/messages";
+export {
+	type BranchSummaryEntry,
+	buildSessionContext,
+	type CompactionEntry,
+	CURRENT_SESSION_VERSION,
+	type CustomEntry,
+	type CustomMessageEntry,
+	type FileEntry,
+	getLatestCompactionEntry,
+	type ModelChangeEntry,
+	migrateSessionEntries,
+	type NewSessionOptions,
+	parseSessionEntries,
+	type SessionContext,
+	type SessionEntry,
+	type SessionEntryBase,
+	type SessionHeader,
+	type SessionInfo,
+	SessionManager,
+	type SessionMessageEntry,
+	type ThinkingLevelChangeEntry,
+} from "./session/session-manager";
+// Tools (detail types and utilities)
+export {
+	type BashToolDetails,
+	DEFAULT_MAX_BYTES,
+	DEFAULT_MAX_LINES,
+	type FindOperations,
+	type FindToolDetails,
+	type FindToolOptions,
+	formatSize,
+	type GrepOperations,
+	type GrepToolDetails,
+	type GrepToolOptions,
+	type LsOperations,
+	type LsToolDetails,
+	type LsToolOptions,
+	type PythonToolDetails,
+	type ReadToolDetails,
+	type TruncationOptions,
+	type TruncationResult,
+	truncateHead,
+	truncateLine,
+	truncateTail,
+	type WriteToolDetails,
+} from "./tools/index";
 export { getShellConfig } from "./utils/shell";
@@ -9,7 +9,7 @@
 */

 import * as path from "node:path";
-import type { Skill } from "$c/core/skills";
+import type { Skill } from "$c/extensibility/skills";
 import type { InternalResource, InternalUrl, ProtocolHandler } from "./types";

 export interface SkillProtocolOptions {
@@ -6,8 +6,8 @@ import {
 	type KernelExecuteResult,
 	type PreludeHelper,
 	PythonKernel,
-} from "./python-kernel";
-import { OutputSink } from "./streaming-output";
+} from "$c/ipy/kernel";
+import { OutputSink } from "$c/session/streaming-output";
 export type PythonKernelMode = "session" | "per-call";

 export interface PythonExecutorOptions {
@@ -5,10 +5,10 @@ import { $, type Subprocess } from "bun";
 import { nanoid } from "nanoid";
 import { getShellConfig, killProcessTree } from "$c/utils/shell";
 import { getOrCreateSnapshot } from "$c/utils/shell-snapshot";
-import { acquireSharedGateway, releaseSharedGateway } from "./python-gateway-coordinator";
-import { loadPythonModules } from "./python-modules";
-import { PYTHON_PRELUDE } from "./python-prelude";
-import { htmlToBasicMarkdown } from "./tools/web-scrapers/types";
+import { htmlToBasicMarkdown } from "$c/web/scrapers/types";
+import { acquireSharedGateway, releaseSharedGateway } from "./gateway-coordinator";
+import { loadPythonModules } from "./modules";
+import { PYTHON_PRELUDE } from "./prelude";

 const TEXT_ENCODER = new TextEncoder();
 const TEXT_DECODER = new TextDecoder();
@@ -0,0 +1,3 @@
+import pythonPrelude from "./prelude.py" with { type: "text" };
+
+export const PYTHON_PRELUDE = pythonPrelude;
@@ -1,6 +1,6 @@
 import * as fs from "node:fs";
 import { logger } from "@oh-my-pi/pi-utils";
-import { ToolAbortError, throwIfAborted } from "$c/core/tool-errors";
+import { ToolAbortError, throwIfAborted } from "$c/tools/tool-errors";
 import { applyWorkspaceEdit } from "./edits";
 import { getLspmuxCommand, isLspmuxSupported } from "./lspmux";
 import type {
@@ -4,7 +4,7 @@
 */

 import path from "node:path";
-import type { Diagnostic, DiagnosticSeverity, LinterClient, ServerConfig } from "$c/core/tools/lsp/types";
+import type { Diagnostic, DiagnosticSeverity, LinterClient, ServerConfig } from "$c/lsp/types";

 // =============================================================================
 // Biome JSON Output Types
@@ -8,7 +8,7 @@
 export { BiomeClient } from "./biome-client";
 export { LspLinterClient } from "./lsp-linter-client";

-import type { LinterClient, ServerConfig } from "$c/core/tools/lsp/types";
+import type { LinterClient, ServerConfig } from "$c/lsp/types";
 import { LspLinterClient } from "./lsp-linter-client";

 // Cache of linter clients by server name + cwd
@@ -3,10 +3,10 @@
 * Uses the Language Server Protocol for formatting and diagnostics.
 */

-import { getOrCreateClient, notifySaved, sendRequest, syncContent } from "$c/core/tools/lsp/client";
-import { applyTextEditsToString } from "$c/core/tools/lsp/edits";
-import type { Diagnostic, LinterClient, LspClient, ServerConfig, TextEdit } from "$c/core/tools/lsp/types";
-import { fileToUri } from "$c/core/tools/lsp/utils";
+import { getOrCreateClient, notifySaved, sendRequest, syncContent } from "$c/lsp/client";
+import { applyTextEditsToString } from "$c/lsp/edits";
+import type { Diagnostic, LinterClient, LspClient, ServerConfig, TextEdit } from "$c/lsp/types";
+import { fileToUri } from "$c/lsp/utils";

 /** Default formatting options for LSP */
 const DEFAULT_FORMAT_OPTIONS = {
@@ -4,12 +4,12 @@ import path from "node:path";
 import type { AgentTool, AgentToolContext, AgentToolResult, AgentToolUpdateCallback } from "@oh-my-pi/pi-agent-core";
 import { logger, once, untilAborted } from "@oh-my-pi/pi-utils";
 import type { BunFile } from "bun";
-import { renderPromptTemplate } from "$c/core/prompt-templates";
-import { throwIfAborted } from "$c/core/tool-errors";
-import type { ToolSession } from "$c/core/tools/index";
-import { resolveToCwd } from "$c/core/tools/path-utils";
-import { type Theme, theme } from "$c/modes/interactive/theme/theme";
+import { renderPromptTemplate } from "$c/config/prompt-templates";
+import { type Theme, theme } from "$c/modes/theme/theme";
 import lspDescription from "$c/prompts/tools/lsp.md" with { type: "text" };
+import type { ToolSession } from "$c/tools/index";
+import { resolveToCwd } from "$c/tools/path-utils";
+import { throwIfAborted } from "$c/tools/tool-errors";
 import {
 	ensureFileOpen,
 	getActiveClients,
@@ -11,8 +11,8 @@
 import type { AgentToolResult, RenderResultOptions } from "@oh-my-pi/pi-agent-core";
 import { Text } from "@oh-my-pi/pi-tui";
 import { highlight, supportsLanguage } from "cli-highlight";
-import { formatExpandHint, formatMoreItems, TRUNCATE_LENGTHS, truncate } from "$c/core/tools/render-utils";
-import { getLanguageFromPath, type Theme } from "$c/modes/interactive/theme/theme";
+import { getLanguageFromPath, type Theme } from "$c/modes/theme/theme";
+import { formatExpandHint, formatMoreItems, TRUNCATE_LENGTHS, truncate } from "$c/tools/render-utils";
 import type { LspParams, LspToolDetails } from "./types";

 // =============================================================================
--- a/Show More
+++ b/Show More