refactor: consolidated module import paths

- Removed custom TypeScript path aliases and the associated transformation script. - Replaced aliased imports with direct `@oh-my-pi` package imports for improved clarity. - Simplified internal module references by removing explicit `/index` suffixes.
2026-01-23 12:48:06 +00:00
parent 0cab1fbce9
commit fcbfab765b
159 changed files with 307 additions and 406 deletions
@@ -14,7 +14,7 @@ This repo contains multiple packages, but **`packages/coding-agent/`** is the pr
 | `packages/agent` | Agent runtime with tool calling and state management |
 | `packages/coding-agent` | Main CLI application (primary focus) |
 | `packages/tui` | Terminal UI library with differential rendering |
-| `packages/omp-stats` | Local observability dashboard (`omp stats`) |
+| `packages/stats` | Local observability dashboard (`omp stats`) |
 | `packages/pi-utils` | Shared utilities (logger, streams, temp files) |

 ## Code Quality
@@ -78,6 +78,18 @@ Download binaries directly from [GitHub Releases](https://github.com/can1357/oh-

 ---

+## + Commit Tool (AI-Powered Git Commits)
+
+AI-powered conventional commit generation with intelligent change analysis:
+
+- **Agentic mode**: Tool-based git inspection with `git-overview`, `git-file-diff`, `git-hunk` for fine-grained analysis
+- **Split commits**: Automatically separates unrelated changes into atomic commits with dependency ordering
+- **Hunk-level staging**: Stage individual hunks when changes span multiple concerns
+- **Changelog generation**: Proposes and applies changelog entries to `CHANGELOG.md` files
+- **Commit validation**: Detects filler words, meta phrases, and enforces conventional commit format
+- **Legacy mode**: `--legacy` flag for deterministic pipeline when preferred
+- Run via `omp commit` with options: `--push`, `--dry-run`, `--no-changelog`, `--context`
+
 ## + Python Tool (IPython Kernel)

 <p align="center">
@@ -93,6 +105,7 @@ Execute Python code with a persistent IPython kernel and 30+ shell-like helpers:
 - **Shared gateway**: Resource-efficient kernel reuse across sessions (`python.sharedGateway` setting)
 - **Custom modules**: Load extensions from `.omp/modules/` and `.pi/modules/` directories
 - **Rich output**: Supports `display()` for HTML, Markdown, images, and interactive JSON trees
+- **Mermaid diagrams**: Renders mermaid code blocks as inline graphics in iTerm2/Kitty terminals
 - Install dependencies via `omp setup python`

 ## + LSP Integration (Language Server Protocol)
@@ -151,6 +164,7 @@ Parallel execution framework with specialized agents and real-time streaming:
 - **Parallel exploration**: Reviewer agent can spawn explore agents for large codebase analysis
 - **Real-time artifact streaming**: Task outputs stream as they're created, not just at completion
 - **Output tool**: Read full agent outputs by ID when truncated previews aren't sufficient
+- **Isolated execution**: `isolated: true` runs tasks in git worktrees, generates patches, and applies cleanly
 - User-level (`~/.omp/agent/agents/`) and project-level (`.omp/agents/`) custom agents
 - Concurrency-limited batch execution with progress tracking

@@ -331,7 +345,7 @@ Handles whitespace and indentation variance automatically:
 | **[@oh-my-pi/pi-agent-core](packages/agent)**          | Agent runtime with tool calling and state management                          |
 | **[@oh-my-pi/pi-coding-agent](packages/coding-agent)** | Interactive coding agent CLI                                                  |
 | **[@oh-my-pi/pi-tui](packages/tui)**                   | Terminal UI library with differential rendering                               |
-| **[@oh-my-pi/omp-stats](packages/omp-stats)**          | Local observability dashboard for AI usage statistics                         |
+| **[@oh-my-pi/omp-stats](packages/stats)**          | Local observability dashboard for AI usage statistics                         |

 ---

@@ -22,7 +22,7 @@
    },
    "packages/agent": {
      "name": "@oh-my-pi/pi-agent-core",
-      "version": "8.0.0",
+      "version": "8.1.0",
      "dependencies": {
        "@oh-my-pi/pi-ai": "workspace:*",
        "@oh-my-pi/pi-tui": "workspace:*",
@@ -36,7 +36,7 @@
    },
    "packages/ai": {
      "name": "@oh-my-pi/pi-ai",
-      "version": "8.0.0",
+      "version": "8.1.0",
      "bin": {
        "pi-ai": "./src/cli.ts",
      },
@@ -64,7 +64,7 @@
    },
    "packages/coding-agent": {
      "name": "@oh-my-pi/pi-coding-agent",
-      "version": "8.0.0",
+      "version": "8.1.0",
      "bin": {
        "omp": "src/cli.ts",
      },
@@ -100,9 +100,9 @@
        "ms": "^2.1.3",
      },
    },
-    "packages/omp-stats": {
+    "packages/stats": {
      "name": "@oh-my-pi/omp-stats",
-      "version": "8.0.0",
+      "version": "8.1.0",
      "bin": {
        "omp-stats": "./src/index.ts",
      },
@@ -122,7 +122,7 @@
    },
    "packages/pi-utils": {
      "name": "@oh-my-pi/pi-utils",
-      "version": "8.0.0",
+      "version": "8.1.0",
      "dependencies": {
        "strip-ansi": "^7.1.2",
        "winston": "^3.17.0",
@@ -151,7 +151,7 @@
    },
    "packages/tui": {
      "name": "@oh-my-pi/pi-tui",
-      "version": "8.0.0",
+      "version": "8.1.0",
      "dependencies": {
        "@types/mime-types": "^2.1.4",
        "chalk": "^5.5.0",
@@ -340,7 +340,7 @@

    "@modelcontextprotocol/sdk": ["@modelcontextprotocol/sdk@1.25.3", "", { "dependencies": { "@hono/node-server": "^1.19.9", "ajv": "^8.17.1", "ajv-formats": "^3.0.1", "content-type": "^1.0.5", "cors": "^2.8.5", "cross-spawn": "^7.0.5", "eventsource": "^3.0.2", "eventsource-parser": "^3.0.0", "express": "^5.0.1", "express-rate-limit": "^7.5.0", "jose": "^6.1.1", "json-schema-typed": "^8.0.2", "pkce-challenge": "^5.0.0", "raw-body": "^3.0.0", "zod": "^3.25 || ^4.0", "zod-to-json-schema": "^3.25.0" }, "peerDependencies": { "@cfworker/json-schema": "^4.1.1" }, "optionalPeers": ["@cfworker/json-schema"] }, "sha512-vsAMBMERybvYgKbg/l4L1rhS7VXV1c0CtyJg72vwxONVX0l4ZfKVAnZEWTQixJGTzKnELjQ59e4NbdFDALRiAQ=="],

-    "@oh-my-pi/omp-stats": ["@oh-my-pi/omp-stats@workspace:packages/omp-stats"],
+    "@oh-my-pi/omp-stats": ["@oh-my-pi/omp-stats@workspace:packages/stats"],

    "@oh-my-pi/pi-agent-core": ["@oh-my-pi/pi-agent-core@workspace:packages/agent"],

@@ -9,7 +9,7 @@
 		"install:dev": "bun install && bun packages/coding-agent/scripts/generate-wasm-b64.ts && bun --cwd=packages/coding-agent link && bun --cwd=packages/ai link",
 		"dev": "bun packages/coding-agent/src/cli.ts",
 		"stats": "bun --cwd=packages/coding-agent src/cli.ts stats",
-		"check": "biome check --write . && bun --cwd=packages/coding-agent run check && bun --cwd=packages/omp-stats run check",
+		"check": "biome check --write . && bun --cwd=packages/coding-agent run check && bun --cwd=packages/stats run check",
 		"fix": "biome check --write --unsafe . && bun --cwd=packages/coding-agent run format-prompts",
 		"bench:gen-fixtures": "bun run packages/react-edit-benchmark/generate.ts --react-dir /tmp/react-source --count-per-type 3",
 		"bench:edit": "bun --cwd=packages/react-edit-benchmark run start",
@@ -1,6 +1,6 @@
 {
 	"name": "@oh-my-pi/pi-agent-core",
-	"version": "8.0.0",
+	"version": "8.1.0",
 	"description": "General-purpose agent with transport abstraction, state management, and attachment support",
 	"type": "module",
 	"main": "./src/index.ts",
@@ -1,3 +1,13 @@
+import { agentLoop, agentLoopContinue } from "@oh-my-pi/pi-agent-core/agent-loop";
+import type {
+	AgentContext,
+	AgentEvent,
+	AgentLoopConfig,
+	AgentMessage,
+	AgentTool,
+	AgentToolContext,
+	ToolCallContext,
+} from "@oh-my-pi/pi-agent-core/types";
 import {
 	type AssistantMessage,
 	type AssistantMessageEvent,
@@ -8,16 +18,6 @@ import {
 } from "@oh-my-pi/pi-ai";
 import { Type } from "@sinclair/typebox";
 import { describe, expect, it } from "vitest";
-import { agentLoop, agentLoopContinue } from "$agent/agent-loop";
-import type {
-	AgentContext,
-	AgentEvent,
-	AgentLoopConfig,
-	AgentMessage,
-	AgentTool,
-	AgentToolContext,
-	ToolCallContext,
-} from "$agent/types";

 // Mock stream for testing - mimics MockAssistantStream
 class MockAssistantStream extends EventStream<AssistantMessageEvent, AssistantMessage> {
@@ -1,3 +1,4 @@
+import { Agent } from "@oh-my-pi/pi-agent-core";
 import {
 	type AssistantMessage,
 	type AssistantMessageEvent,
@@ -7,7 +8,6 @@ import {
 	type Usage,
 } from "@oh-my-pi/pi-ai";
 import { describe, expect, it } from "vitest";
-import { Agent } from "$agent/index";

 class MockAssistantStream extends EventStream<AssistantMessageEvent, AssistantMessage> {
 	constructor() {
@@ -1,7 +1,7 @@
+import { Agent } from "@oh-my-pi/pi-agent-core";
 import type { AssistantMessage, Model, ToolResultMessage, UserMessage } from "@oh-my-pi/pi-ai";
 import { getModel } from "@oh-my-pi/pi-ai";
 import { describe, expect, it } from "vitest";
-import { Agent } from "$agent/index";
 import { calculateTool } from "./utils/calculate";

 async function basicPrompt(model: Model<any>) {
@@ -1,5 +1,5 @@
+import type { AgentTool, AgentToolResult } from "@oh-my-pi/pi-agent-core/types";
 import { type Static, Type } from "@sinclair/typebox";
-import type { AgentTool, AgentToolResult } from "$agent/types";

 export interface CalculateResult extends AgentToolResult<undefined> {
 	content: Array<{ type: "text"; text: string }>;
@@ -1,5 +1,5 @@
+import type { AgentTool, AgentToolResult } from "@oh-my-pi/pi-agent-core/types";
 import { type Static, Type } from "@sinclair/typebox";
-import type { AgentTool, AgentToolResult } from "$agent/types";

 export interface GetCurrentTimeResult extends AgentToolResult<{ utcTimestamp: number }> {}

@@ -4,11 +4,6 @@
 		"noEmit": true,
 		"baseUrl": ".",
 		"paths": {
-			"$agent/*": ["./src/*"],
-			"$ai/*": ["../ai/src/*"],
-			"$c/*": ["../coding-agent/src/*"],
-			"$tui/*": ["../tui/src/*"],
-			"$stats/*": ["../omp-stats/src/*"],
 			"@oh-my-pi/pi-agent-core": ["./src/index.ts"],
 			"@oh-my-pi/pi-agent-core/*": ["./src/*"],
 			"@oh-my-pi/pi-ai": ["../ai/src/index.ts"],
@@ -1,6 +1,6 @@
 {
 	"name": "@oh-my-pi/pi-ai",
-	"version": "8.0.0",
+	"version": "8.1.0",
 	"description": "Unified LLM API with automatic model discovery and provider configuration",
 	"type": "module",
 	"main": "./src/index.ts",
@@ -20,16 +20,18 @@
 		}
 	},
 	"bin": {
-		"pi-ai": "./src/cli.ts"
+		"pi-ai": "./dist/cli.js"
 	},
 	"files": [
+		"dist",
 		"src",
 		"README.md"
 	],
 	"scripts": {
+		"build": "tsgo -p tsconfig.build.json",
 		"generate-models": "bun scripts/generate-models.ts",
 		"test": "bun test",
-		"prepublishOnly": "cp tsconfig.publish.json tsconfig.json"
+		"prepublishOnly": "cp tsconfig.publish.json tsconfig.json && bun run build"
 	},
 	"dependencies": {
 		"@oh-my-pi/pi-utils": "workspace:*",
@@ -2,12 +2,12 @@
 import { createInterface } from "readline";
 import { CliAuthStorage } from "./storage";
 import "./utils/migrate-env";
+import { getOAuthProviders } from "./utils/oauth";
 import { loginAnthropic } from "./utils/oauth/anthropic";
 import { loginCursor } from "./utils/oauth/cursor";
 import { loginGitHubCopilot } from "./utils/oauth/github-copilot";
 import { loginAntigravity } from "./utils/oauth/google-antigravity";
 import { loginGeminiCli } from "./utils/oauth/google-gemini-cli";
-import { getOAuthProviders } from "./utils/oauth/index";
 import { loginOpenAICodex } from "./utils/oauth/openai-codex";
 import type { OAuthCredentials, OAuthProvider } from "./utils/oauth/types";

@@ -18,7 +18,7 @@ export * from "./usage/google-antigravity";
 export * from "./usage/openai-codex";
 export * from "./usage/zai";
 export * from "./utils/event-stream";
-export * from "./utils/oauth/index";
+export * from "./utils/oauth";
 export * from "./utils/overflow";
 export * from "./utils/retry";
 export * from "./utils/typebox-helpers";
@@ -1,7 +1,7 @@
 import { readFileSync } from "node:fs";
 import { join } from "node:path";
-import type { Api, Context, Model, Tool, ToolResultMessage } from "@oh-my-pi/pi-ai/index";
-import { complete, getModel } from "@oh-my-pi/pi-ai/index";
+import type { Api, Context, Model, Tool, ToolResultMessage } from "@oh-my-pi/pi-ai";
+import { complete, getModel } from "@oh-my-pi/pi-ai";
 import type { OptionsForApi } from "@oh-my-pi/pi-ai/types";
 import { Type } from "@sinclair/typebox";
 import { describe, expect, it } from "vitest";
@@ -6,7 +6,7 @@
 */

 import { chmodSync, existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
-import { getOAuthApiKey } from "@oh-my-pi/pi-ai/utils/oauth/index";
+import { getOAuthApiKey } from "@oh-my-pi/pi-ai/utils/oauth";
 import type { OAuthCredentials, OAuthProvider } from "@oh-my-pi/pi-ai/utils/oauth/types";
 import { homedir } from "os";
 import { dirname, join } from "path";
@@ -4,11 +4,6 @@
 		"noEmit": true,
 		"baseUrl": ".",
 		"paths": {
-			"$ai/*": ["./src/*"],
-			"$c/*": ["../coding-agent/src/*"],
-			"$tui/*": ["../tui/src/*"],
-			"$agent/*": ["../agent/src/*"],
-			"$stats/*": ["../omp-stats/src/*"],
 			"@oh-my-pi/pi-ai": ["./src/index.ts"],
 			"@oh-my-pi/pi-ai/*": ["./src/*"],
 			"@oh-my-pi/pi-agent-core": ["../agent/src/index.ts"],
@@ -1,6 +1,6 @@
 {
 	"name": "@oh-my-pi/pi-coding-agent",
-	"version": "8.0.0",
+	"version": "8.1.0",
 	"description": "Coding agent CLI with read, bash, edit, write tools and session management",
 	"type": "module",
 	"ompConfig": {
@@ -5,7 +5,7 @@
 * persistent guidance to the agent.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * TypeScript/JavaScript extension modules loaded by the extension system.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * Gemini-style extensions that provide MCP servers, tools, and context.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { MCPServer } from "./mcp";
 import type { SourceMeta } from "./types";

@@ -4,7 +4,7 @@
 * Pre/post tool execution hooks defined as shell scripts.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * GitHub Copilot-style instructions with optional file pattern matching.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -5,7 +5,7 @@
 * All providers translate their native format to this shape.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * Reusable prompt templates (Codex format) available via /prompts: menu.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -5,7 +5,7 @@
 * Translated to a canonical shape regardless of source format.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * Configuration settings from various sources (JSON, TOML, etc.)
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * Skills provide specialized knowledge or workflows that extend agent capabilities.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * File-based slash commands defined as markdown files.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * Canonical shape for SSH host entries, regardless of source format.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -5,7 +5,7 @@
 * Distinct from context-files which are user instructions shown in conversation.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@
 * User-defined tools that extend agent capabilities.
 */

-import { defineCapability } from "./index";
+import { defineCapability } from ".";
 import type { SourceMeta } from "./types";

 /**
@@ -4,7 +4,7 @@

 import type { ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import { APP_NAME, CONFIG_DIR_NAME, ENV_AGENT_DIR } from "@oh-my-pi/pi-coding-agent/config";
-import { BUILTIN_TOOLS } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { BUILTIN_TOOLS } from "@oh-my-pi/pi-coding-agent/tools";
 import chalk from "chalk";

 export type Mode = "text" | "json" | "rpc";
@@ -5,11 +5,7 @@
 */

 import { APP_NAME } from "@oh-my-pi/pi-coding-agent/config";
-import {
-	PluginManager,
-	parseSettingValue,
-	validateSetting,
-} from "@oh-my-pi/pi-coding-agent/extensibility/plugins/index";
+import { PluginManager, parseSettingValue, validateSetting } from "@oh-my-pi/pi-coding-agent/extensibility/plugins";
 import { theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import chalk from "chalk";

@@ -9,7 +9,7 @@ import type { CustomTool, CustomToolContext } from "@oh-my-pi/pi-coding-agent/ex
 import type { AuthStorage } from "@oh-my-pi/pi-coding-agent/session/auth-storage";
 import { TaskTool } from "@oh-my-pi/pi-coding-agent/task";
 import type { TaskParams } from "@oh-my-pi/pi-coding-agent/task/types";
-import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { Type } from "@sinclair/typebox";

 const analyzeFileSchema = Type.Object({
@@ -79,16 +79,6 @@ export function getAuthPath(): string {
 	return join(getAgentDir(), "auth.json");
 }

-/** Get path to settings.json (legacy, use getConfigPath for config.yaml) */
-export function getLegacySettingsPath(): string {
-	return join(getAgentDir(), "settings.json");
-}
-
-/** Get path to config.yml (user settings) */
-export function getConfigPath(): string {
-	return join(getAgentDir(), "config.yml");
-}
-
 /**
 * Gets the path to agent.db (SQLite database for settings and auth storage).
 * @param agentDir - Base agent directory, defaults to ~/.omp/agent
@@ -2,7 +2,7 @@ import { existsSync, readFileSync } from "node:fs";
 import { rename } from "node:fs/promises";
 import { join } from "node:path";
 import { type Settings as SettingsItem, settingsCapability } from "@oh-my-pi/pi-coding-agent/capability/settings";
-import { getAgentDbPath, getAgentDir, getConfigPath } from "@oh-my-pi/pi-coding-agent/config";
+import { getAgentDbPath, getAgentDir } from "@oh-my-pi/pi-coding-agent/config";
 import { withFileLock } from "@oh-my-pi/pi-coding-agent/config/file-lock";
 import { loadCapability } from "@oh-my-pi/pi-coding-agent/discovery";
 import type { SymbolPreset } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
@@ -503,7 +503,7 @@ export class SettingsManager {
 	 * @returns Configured SettingsManager with merged global and user settings
 	 */
 	static async create(cwd: string = process.cwd(), agentDir: string = getAgentDir()): Promise<SettingsManager> {
-		const configPath = getConfigPath();
+		const configPath = join(agentDir, "config.yml");
 		const storage = await AgentStorage.open(getAgentDbPath(agentDir));

 		// Migrate from legacy storage if config.yml doesn't exist
@@ -7,9 +7,9 @@
 */

 import { dirname, join, sep } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { type ContextFile, contextFileCapability } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import type { LoadContext, LoadResult } from "@oh-my-pi/pi-coding-agent/capability/types";
 import { calculateDepth, createSourceMeta } from "./helpers";

@@ -5,6 +5,7 @@
 * .pi is an alias for backwards compatibility.
 */

+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { type ContextFile, contextFileCapability } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import {
 	type Extension,
@@ -14,7 +15,6 @@ import {
 import { type ExtensionModule, extensionModuleCapability } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
 import { readDirEntries, readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
 import { type Hook, hookCapability } from "@oh-my-pi/pi-coding-agent/capability/hook";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type Instruction, instructionCapability } from "@oh-my-pi/pi-coding-agent/capability/instruction";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import { type Prompt, promptCapability } from "@oh-my-pi/pi-coding-agent/capability/prompt";
@@ -6,11 +6,11 @@
 */

 import { join, sep } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { type ContextFile, contextFileCapability } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import { type ExtensionModule, extensionModuleCapability } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
 import { type Hook, hookCapability } from "@oh-my-pi/pi-coding-agent/capability/hook";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import { type Settings, settingsCapability } from "@oh-my-pi/pi-coding-agent/capability/settings";
 import { type Skill, skillCapability } from "@oh-my-pi/pi-coding-agent/capability/skill";
@@ -6,8 +6,8 @@
 */

 import { dirname, resolve } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { readDirEntries, readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import type { Rule } from "@oh-my-pi/pi-coding-agent/capability/rule";
 import { ruleCapability } from "@oh-my-pi/pi-coding-agent/capability/rule";
 import type { LoadContext, LoadResult } from "@oh-my-pi/pi-coding-agent/capability/types";
@@ -8,13 +8,13 @@
 */

 import { join } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import type { ContextFile } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import { contextFileCapability } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import { type ExtensionModule, extensionModuleCapability } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
 import type { Hook } from "@oh-my-pi/pi-coding-agent/capability/hook";
 import { hookCapability } from "@oh-my-pi/pi-coding-agent/capability/hook";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import type { MCPServer } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import { mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import type { Prompt } from "@oh-my-pi/pi-coding-agent/capability/prompt";
@@ -14,8 +14,8 @@
 * - settings: From settings.json if present
 */

+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import type { Rule } from "@oh-my-pi/pi-coding-agent/capability/rule";
 import { ruleCapability } from "@oh-my-pi/pi-coding-agent/capability/rule";
@@ -17,6 +17,7 @@
 */

 import { join, sep } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { type ContextFile, contextFileCapability } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import {
 	type Extension,
@@ -25,7 +26,6 @@ import {
 } from "@oh-my-pi/pi-coding-agent/capability/extension";
 import { type ExtensionModule, extensionModuleCapability } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
 import { readDirEntries, readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import { type Settings, settingsCapability } from "@oh-my-pi/pi-coding-agent/capability/settings";
 import { type SystemPrompt, systemPromptCapability } from "@oh-my-pi/pi-coding-agent/capability/system-prompt";
@@ -13,9 +13,9 @@
 */

 import { basename, dirname, sep } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { type ContextFile, contextFileCapability } from "@oh-my-pi/pi-coding-agent/capability/context-file";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type Instruction, instructionCapability } from "@oh-my-pi/pi-coding-agent/capability/instruction";
 import type { LoadContext, LoadResult, SourceMeta } from "@oh-my-pi/pi-coding-agent/capability/types";
 import { parseFrontmatter } from "@oh-my-pi/pi-coding-agent/utils/frontmatter";
@@ -17,28 +17,24 @@ import "../capability/rule";
 import "../capability/settings";
 import "../capability/skill";
 import "../capability/slash-command";
-import "../capability/system-prompt";
 import "../capability/ssh";
+import "../capability/system-prompt";
 import "../capability/tool";

 // Import providers (each registers itself on import)
+import "./agents-md";
 import "./builtin";
 import "./claude";
-import "./codex";
-import "./gemini";
-import "./cursor";
-import "./windsurf";
 import "./cline";
+import "./codex";
+import "./cursor";
+import "./gemini";
 import "./github";
-import "./vscode";
-import "./agents-md";
 import "./mcp-json";
 import "./ssh";
+import "./vscode";
+import "./windsurf";

-export type { ContextFile } from "@oh-my-pi/pi-coding-agent/capability/context-file";
-export type { Extension, ExtensionManifest } from "@oh-my-pi/pi-coding-agent/capability/extension";
-export type { ExtensionModule } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
-export type { Hook } from "@oh-my-pi/pi-coding-agent/capability/hook";
 // Re-export the main API from capability registry
 export {
 	cacheStats,
@@ -62,7 +58,11 @@ export {
 	// Cache management
 	reset,
 	setDisabledProviders,
-} from "@oh-my-pi/pi-coding-agent/capability/index";
+} from "@oh-my-pi/pi-coding-agent/capability";
+export type { ContextFile } from "@oh-my-pi/pi-coding-agent/capability/context-file";
+export type { Extension, ExtensionManifest } from "@oh-my-pi/pi-coding-agent/capability/extension";
+export type { ExtensionModule } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
+export type { Hook } from "@oh-my-pi/pi-coding-agent/capability/hook";
 export type { Instruction } from "@oh-my-pi/pi-coding-agent/capability/instruction";
 // Re-export capability item types
 export type { MCPServer } from "@oh-my-pi/pi-coding-agent/capability/mcp";
@@ -8,8 +8,8 @@
 */

 import { join } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import type { LoadContext, LoadResult, SourceMeta } from "@oh-my-pi/pi-coding-agent/capability/types";
 import { createSourceMeta, expandEnvVarsDeep, parseJSON } from "./helpers";
@@ -6,8 +6,8 @@
 */

 import { join } from "node:path";
+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type SSHHost, sshCapability } from "@oh-my-pi/pi-coding-agent/capability/ssh";
 import type { LoadContext, LoadResult, SourceMeta } from "@oh-my-pi/pi-coding-agent/capability/types";
 import { createSourceMeta, expandEnvVarsDeep, parseJSON } from "./helpers";
@@ -5,8 +5,8 @@
 * Supports MCP server discovery from `mcp.json` with nested `mcp.servers` structure.
 */

+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import type { LoadContext, LoadResult } from "@oh-my-pi/pi-coding-agent/capability/types";
 import { createSourceMeta, expandEnvVarsDeep, getProjectPath, parseJSON } from "./helpers";
@@ -11,8 +11,8 @@
 * - Legacy .windsurfrules file
 */

+import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability";
 import { readFile } from "@oh-my-pi/pi-coding-agent/capability/fs";
-import { registerProvider } from "@oh-my-pi/pi-coding-agent/capability/index";
 import { type MCPServer, mcpCapability } from "@oh-my-pi/pi-coding-agent/capability/mcp";
 import { type Rule, ruleCapability } from "@oh-my-pi/pi-coding-agent/capability/rule";
 import type { LoadContext, LoadResult } from "@oh-my-pi/pi-coding-agent/capability/types";
@@ -7,9 +7,9 @@

 import { type Dirent, existsSync, readdirSync } from "node:fs";
 import * as path from "node:path";
+import * as piCodingAgent from "@oh-my-pi/pi-coding-agent";
 import { getAgentDir, getConfigDirs } from "@oh-my-pi/pi-coding-agent/config";
 import { execCommand } from "@oh-my-pi/pi-coding-agent/exec/exec";
-import * as piCodingAgent from "@oh-my-pi/pi-coding-agent/index";
 import { logger } from "@oh-my-pi/pi-utils";
 import * as typebox from "@sinclair/typebox";
 import { ReviewCommand } from "./bundled/review";
@@ -23,7 +23,7 @@ export interface CustomCommandAPI {
 	/** Injected @sinclair/typebox module */
 	typebox: typeof import("@sinclair/typebox");
 	/** Injected pi-coding-agent exports */
-	pi: typeof import("../../index");
+	pi: typeof import("../..");
 }

 /**
@@ -6,6 +6,7 @@
 */

 import * as path from "node:path";
+import * as piCodingAgent from "@oh-my-pi/pi-coding-agent";
 import { toolCapability } from "@oh-my-pi/pi-coding-agent/capability/tool";
 import { type CustomTool, loadCapability } from "@oh-my-pi/pi-coding-agent/discovery";
 import { expandPath } from "@oh-my-pi/pi-coding-agent/discovery/helpers";
@@ -13,7 +14,6 @@ import type { ExecOptions } from "@oh-my-pi/pi-coding-agent/exec/exec";
 import { execCommand } from "@oh-my-pi/pi-coding-agent/exec/exec";
 import type { HookUIContext } from "@oh-my-pi/pi-coding-agent/extensibility/hooks/types";
 import { getAllPluginToolPaths } from "@oh-my-pi/pi-coding-agent/extensibility/plugins/loader";
-import * as piCodingAgent from "@oh-my-pi/pi-coding-agent/index";
 import { theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import { logger } from "@oh-my-pi/pi-utils";
 import * as typebox from "@sinclair/typebox";
@@ -39,7 +39,7 @@ export interface CustomToolAPI {
 	/** Injected @sinclair/typebox module */
 	typebox: typeof import("@sinclair/typebox");
 	/** Injected pi-coding-agent exports */
-	pi: typeof import("../../index");
+	pi: typeof import("../..");
 }

 /**
@@ -6,12 +6,12 @@ import { existsSync, readdirSync, readFileSync, statSync } from "node:fs";
 import * as path from "node:path";
 import type { ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import type { ImageContent, Model, TextContent } from "@oh-my-pi/pi-ai";
+import * as piCodingAgent from "@oh-my-pi/pi-coding-agent";
 import { type ExtensionModule, extensionModuleCapability } from "@oh-my-pi/pi-coding-agent/capability/extension-module";
 import { loadCapability } from "@oh-my-pi/pi-coding-agent/discovery";
 import { expandPath, getExtensionNameFromPath } from "@oh-my-pi/pi-coding-agent/discovery/helpers";
 import type { ExecOptions } from "@oh-my-pi/pi-coding-agent/exec/exec";
 import { execCommand } from "@oh-my-pi/pi-coding-agent/exec/exec";
-import * as piCodingAgent from "@oh-my-pi/pi-coding-agent/index";
 import type { CustomMessage } from "@oh-my-pi/pi-coding-agent/session/messages";
 import { EventBus } from "@oh-my-pi/pi-coding-agent/utils/event-bus";
 import type { KeyId } from "@oh-my-pi/pi-tui";
@@ -10,11 +10,11 @@

 import type { AgentMessage, AgentToolResult, AgentToolUpdateCallback, ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import type { ImageContent, Model, TextContent, ToolResultMessage } from "@oh-my-pi/pi-ai";
+import type * as piCodingAgent from "@oh-my-pi/pi-coding-agent";
 import type { KeybindingsManager } from "@oh-my-pi/pi-coding-agent/config/keybindings";
 import type { ModelRegistry } from "@oh-my-pi/pi-coding-agent/config/model-registry";
 import type { BashResult } from "@oh-my-pi/pi-coding-agent/exec/bash-executor";
 import type { ExecOptions, ExecResult } from "@oh-my-pi/pi-coding-agent/exec/exec";
-import type * as piCodingAgent from "@oh-my-pi/pi-coding-agent/index";
 import type { PythonResult } from "@oh-my-pi/pi-coding-agent/ipy/executor";
 import type { Theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import type { EditToolDetails } from "@oh-my-pi/pi-coding-agent/patch";
@@ -3,11 +3,11 @@
 */

 import * as path from "node:path";
+import * as piCodingAgent from "@oh-my-pi/pi-coding-agent";
 import { hookCapability } from "@oh-my-pi/pi-coding-agent/capability/hook";
 import type { Hook } from "@oh-my-pi/pi-coding-agent/discovery";
 import { loadCapability } from "@oh-my-pi/pi-coding-agent/discovery";
 import { expandPath } from "@oh-my-pi/pi-coding-agent/discovery/helpers";
-import * as piCodingAgent from "@oh-my-pi/pi-coding-agent/index";
 import type { HookMessage } from "@oh-my-pi/pi-coding-agent/session/messages";
 import type { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
 import { logger } from "@oh-my-pi/pi-utils";
@@ -11,7 +11,7 @@ import type { ModelRegistry } from "@oh-my-pi/pi-coding-agent/config/model-regis
 import type { ExecOptions, ExecResult } from "@oh-my-pi/pi-coding-agent/exec/exec";
 import type { Theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import type { EditToolDetails } from "@oh-my-pi/pi-coding-agent/patch";
-import type { CompactionPreparation, CompactionResult } from "@oh-my-pi/pi-coding-agent/session/compaction/index";
+import type { CompactionPreparation, CompactionResult } from "@oh-my-pi/pi-coding-agent/session/compaction";
 import type { HookMessage } from "@oh-my-pi/pi-coding-agent/session/messages";
 import type {
 	BranchSummaryEntry,
@@ -26,7 +26,7 @@ import type {
 	GrepToolDetails,
 	LsToolDetails,
 	ReadToolDetails,
-} from "@oh-my-pi/pi-coding-agent/tools/index";
+} from "@oh-my-pi/pi-coding-agent/tools";
 import type { Component, TUI } from "@oh-my-pi/pi-tui";

 // Re-export for backward compatibility
@@ -752,7 +752,7 @@ export interface HookAPI {
 	/** Injected @sinclair/typebox module */
 	typebox: typeof import("@sinclair/typebox");
 	/** Injected pi-coding-agent exports */
-	pi: typeof import("../../index");
+	pi: typeof import("../..");
 }

 /**
@@ -3,7 +3,7 @@
 // TypeBox helper for string enums (convenience for custom tools)
 // Re-export from pi-ai which uses the correct enum-based schema format
 export { StringEnum } from "@oh-my-pi/pi-ai";
-export type { FileDiagnosticsResult } from "@oh-my-pi/pi-coding-agent/lsp/index";
+export type { FileDiagnosticsResult } from "@oh-my-pi/pi-coding-agent/lsp";
 // UI components for extensions
 export {
 	ArminComponent,
@@ -37,7 +37,7 @@ export {
 	UserMessageComponent,
 	UserMessageSelectorComponent,
 	type VisualTruncateResult,
-} from "@oh-my-pi/pi-coding-agent/modes/components/index";
+} from "@oh-my-pi/pi-coding-agent/modes/components";
 // Theme utilities for custom tools
 export {
 	getLanguageFromPath,
@@ -88,9 +88,9 @@ export type {
 	ExecResult,
 	LoadedCustomTool,
 	RenderResultOptions,
-} from "./extensibility/custom-tools/index";
+} from "./extensibility/custom-tools";
 // Custom tools
-export { CustomToolLoader, discoverAndLoadCustomTools, loadCustomTools } from "./extensibility/custom-tools/index";
+export { CustomToolLoader, discoverAndLoadCustomTools, loadCustomTools } from "./extensibility/custom-tools";
 export type {
 	AppAction,
 	Extension,
@@ -122,7 +122,7 @@ export type {
 	UserBashEventResult,
 	UserPythonEvent,
 	UserPythonEventResult,
-} from "./extensibility/extensions/index";
+} from "./extensibility/extensions";
 // Extension types and utilities
 export {
 	discoverAndLoadExtensions,
@@ -135,9 +135,9 @@ export {
 	isLsToolResult,
 	isReadToolResult,
 	isWriteToolResult,
-} from "./extensibility/extensions/index";
+} from "./extensibility/extensions";
 // Hook system types (legacy re-export)
-export type * from "./extensibility/hooks/index";
+export type * from "./extensibility/hooks";
 // Skills
 export {
 	type LoadSkillsFromDirOptions,
@@ -162,7 +162,7 @@ export {
 	type RpcEventListener,
 	runPrintMode,
 	runRpcMode,
-} from "./modes/index";
+} from "./modes";
 // SDK for programmatic usage
 export {
 	// Factory
@@ -228,7 +228,7 @@ export {
 	prepareBranchEntries,
 	serializeConversation,
 	shouldCompact,
-} from "./session/compaction/index";
+} from "./session/compaction";
 export { convertToLlm } from "./session/messages";
 export {
 	type BranchSummaryEntry,
@@ -275,5 +275,5 @@ export {
 	truncateLine,
 	truncateTail,
 	type WriteToolDetails,
-} from "./tools/index";
+} from "./tools";
 export { getShellConfig } from "./utils/shell";
@@ -5,7 +5,7 @@ import type { AgentTool, AgentToolContext, AgentToolResult, AgentToolUpdateCallb
 import { renderPromptTemplate } from "@oh-my-pi/pi-coding-agent/config/prompt-templates";
 import { type Theme, theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import lspDescription from "@oh-my-pi/pi-coding-agent/prompts/tools/lsp.md" with { type: "text" };
-import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { resolveToCwd } from "@oh-my-pi/pi-coding-agent/tools/path-utils";
 import { throwIfAborted } from "@oh-my-pi/pi-coding-agent/tools/tool-errors";
 import { logger, once, untilAborted } from "@oh-my-pi/pi-utils";
@@ -28,10 +28,10 @@ import type { ModelRegistry } from "./config/model-registry";
 import { parseModelPattern, parseModelString, resolveModelScope, type ScopedModel } from "./config/model-resolver";
 import { SettingsManager } from "./config/settings-manager";
 import { initializeWithSettings } from "./discovery";
-import { exportFromFile } from "./export/html/index";
+import { exportFromFile } from "./export/html";
 import type { ExtensionUIContext } from "./extensibility/extensions/types";
 import { runMigrations, showDeprecationWarnings } from "./migrations";
-import { InteractiveMode, runPrintMode, runRpcMode } from "./modes/index";
+import { InteractiveMode, runPrintMode, runRpcMode } from "./modes";
 import { type CreateAgentSessionOptions, createAgentSession, discoverAuthStorage, discoverModels } from "./sdk";
 import type { AgentSession } from "./session/agent-session";
 import { type SessionInfo, SessionManager } from "./session/session-manager";
@@ -87,7 +87,7 @@ async function runInteractiveMode(
 	initialMessages: string[],
 	setExtensionUIContext: (uiContext: ExtensionUIContext, hasUI: boolean) => void,
 	lspServers: Array<{ name: string; status: "ready" | "error"; fileTypes: string[] }> | undefined,
-	mcpManager: import("./mcp/index").MCPManager | undefined,
+	mcpManager: import("./mcp").MCPManager | undefined,
 	initialMessage?: string,
 	initialImages?: ImageContent[],
 ): Promise<void> {
@@ -821,7 +821,7 @@ export class TreeSelectorComponent extends Container {
 			new TruncatedText(
 				theme.fg(
 					"muted",
-					"  Up/Down: move. Left/Right: page. Shift+L: label. Ctrl+O/Shift+Ctrl+O: filter. Alt+D/T/U/L/A: filter. Type to search",
+					"Up/Down: move. Left/Right: page. Shift+L: label. Ctrl+O/Shift+Ctrl+O: filter. Alt+D/T/U/L/A: filter. Type to search",
 				),
 				0,
 				0,
@@ -5,7 +5,7 @@ import type {
 	ExtensionContextActions,
 	ExtensionError,
 	ExtensionUIContext,
-} from "@oh-my-pi/pi-coding-agent/extensibility/extensions/index";
+} from "@oh-my-pi/pi-coding-agent/extensibility/extensions";
 import { HookEditorComponent } from "@oh-my-pi/pi-coding-agent/modes/components/hook-editor";
 import { HookInputComponent } from "@oh-my-pi/pi-coding-agent/modes/components/hook-input";
 import { HookSelectorComponent } from "@oh-my-pi/pi-coding-agent/modes/components/hook-selector";
@@ -21,7 +21,7 @@ import {
 } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import type { InteractiveModeContext } from "@oh-my-pi/pi-coding-agent/modes/types";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
-import { setPreferredImageProvider, setPreferredWebSearchProvider } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { setPreferredImageProvider, setPreferredWebSearchProvider } from "@oh-my-pi/pi-coding-agent/tools";
 import type { Component } from "@oh-my-pi/pi-tui";
 import { Input, Loader, Spacer, Text } from "@oh-my-pi/pi-tui";

@@ -8,7 +8,7 @@ import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
 import type { AssistantMessage, ImageContent, Message, UsageReport } from "@oh-my-pi/pi-ai";
 import { KeybindingsManager } from "@oh-my-pi/pi-coding-agent/config/keybindings";
 import type { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manager";
-import type { ExtensionUIContext } from "@oh-my-pi/pi-coding-agent/extensibility/extensions/index";
+import type { ExtensionUIContext } from "@oh-my-pi/pi-coding-agent/extensibility/extensions";
 import type { CompactOptions } from "@oh-my-pi/pi-coding-agent/extensibility/extensions/types";
 import { loadSlashCommands } from "@oh-my-pi/pi-coding-agent/extensibility/slash-commands";
 import type { AgentSession, AgentSessionEvent } from "@oh-my-pi/pi-coding-agent/session/agent-session";
@@ -125,7 +125,7 @@ export class InteractiveMode implements InteractiveModeContext {
 	private readonly changelogMarkdown: string | undefined;
 	public readonly lspServers: Array<{ name: string; status: "ready" | "error"; fileTypes: string[] }> | undefined =
 		undefined;
-	public mcpManager?: import("@oh-my-pi/pi-coding-agent/mcp/index").MCPManager;
+	public mcpManager?: import("@oh-my-pi/pi-coding-agent/mcp").MCPManager;
 	private readonly toolUiContextSetter: (uiContext: ExtensionUIContext, hasUI: boolean) => void;

 	private readonly commandController: CommandController;
@@ -141,7 +141,7 @@ export class InteractiveMode implements InteractiveModeContext {
 		changelogMarkdown: string | undefined = undefined,
 		setToolUIContext: (uiContext: ExtensionUIContext, hasUI: boolean) => void = () => {},
 		lspServers: Array<{ name: string; status: "ready" | "error"; fileTypes: string[] }> | undefined = undefined,
-		mcpManager?: import("@oh-my-pi/pi-coding-agent/mcp/index").MCPManager,
+		mcpManager?: import("@oh-my-pi/pi-coding-agent/mcp").MCPManager,
 	) {
 		this.session = session;
 		this.sessionManager = session.sessionManager;
@@ -8,7 +8,7 @@ import type { AgentEvent, AgentMessage, ThinkingLevel } from "@oh-my-pi/pi-agent
 import type { ImageContent } from "@oh-my-pi/pi-ai";
 import type { BashResult } from "@oh-my-pi/pi-coding-agent/exec/bash-executor";
 import type { SessionStats } from "@oh-my-pi/pi-coding-agent/session/agent-session";
-import type { CompactionResult } from "@oh-my-pi/pi-coding-agent/session/compaction/index";
+import type { CompactionResult } from "@oh-my-pi/pi-coding-agent/session/compaction";
 import { createSanitizerStream, createSplitterStream, createTextDecoderStream, ptree } from "@oh-my-pi/pi-utils";
 import type { RpcCommand, RpcResponse, RpcSessionState } from "./rpc-types";

@@ -11,10 +11,7 @@
 * - Extension UI: Extension UI requests are emitted, client responds with extension_ui_response
 */

-import type {
-	ExtensionUIContext,
-	ExtensionUIDialogOptions,
-} from "@oh-my-pi/pi-coding-agent/extensibility/extensions/index";
+import type { ExtensionUIContext, ExtensionUIDialogOptions } from "@oh-my-pi/pi-coding-agent/extensibility/extensions";
 import { type Theme, theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import type { AgentSession } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import { readLines } from "@oh-my-pi/pi-utils";
@@ -9,7 +9,7 @@ import type { AgentMessage, ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import type { ImageContent, Model } from "@oh-my-pi/pi-ai";
 import type { BashResult } from "@oh-my-pi/pi-coding-agent/exec/bash-executor";
 import type { SessionStats } from "@oh-my-pi/pi-coding-agent/session/agent-session";
-import type { CompactionResult } from "@oh-my-pi/pi-coding-agent/session/compaction/index";
+import type { CompactionResult } from "@oh-my-pi/pi-coding-agent/session/compaction";

 // ============================================================================
 // RPC Commands (stdin)
@@ -2,9 +2,9 @@ import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
 import type { AssistantMessage, ImageContent, Message, UsageReport } from "@oh-my-pi/pi-ai";
 import type { KeybindingsManager } from "@oh-my-pi/pi-coding-agent/config/keybindings";
 import type { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manager";
-import type { ExtensionUIContext } from "@oh-my-pi/pi-coding-agent/extensibility/extensions/index";
+import type { ExtensionUIContext } from "@oh-my-pi/pi-coding-agent/extensibility/extensions";
 import type { CompactOptions } from "@oh-my-pi/pi-coding-agent/extensibility/extensions/types";
-import type { MCPManager } from "@oh-my-pi/pi-coding-agent/mcp/index";
+import type { MCPManager } from "@oh-my-pi/pi-coding-agent/mcp";
 import type { AgentSession, AgentSessionEvent } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import type { HistoryStorage } from "@oh-my-pi/pi-coding-agent/session/history-storage";
 import type { SessionContext, SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
@@ -18,10 +18,10 @@ import {
 	flushLspWritethroughBatch,
 	type WritethroughCallback,
 	writethroughNoop,
-} from "@oh-my-pi/pi-coding-agent/lsp/index";
+} from "@oh-my-pi/pi-coding-agent/lsp";
 import patchDescription from "@oh-my-pi/pi-coding-agent/prompts/tools/patch.md" with { type: "text" };
 import replaceDescription from "@oh-my-pi/pi-coding-agent/prompts/tools/replace.md" with { type: "text" };
-import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { outputMeta } from "@oh-my-pi/pi-coding-agent/tools/output-meta";
 import { resolveToCwd } from "@oh-my-pi/pi-coding-agent/tools/path-utils";
 import { Type } from "@sinclair/typebox";
@@ -48,13 +48,7 @@ export { computeEditDiff, computePatchDiff, generateDiffString, generateUnifiedD
 export { DEFAULT_FUZZY_THRESHOLD, findContextLine, findMatch as findEditMatch, findMatch, seekSequence } from "./fuzzy";

 // Normalization
-export {
-	adjustIndentation,
-	detectLineEnding,
-	normalizeToLF,
-	restoreLineEndings,
-	stripBom,
-} from "./normalize";
+export { adjustIndentation, detectLineEnding, normalizeToLF, restoreLineEndings, stripBom } from "./normalize";

 // Parsing
 export { normalizeCreateContent, normalizeDiff, parseHunks as parseDiffHunks } from "./parser";
@@ -4,7 +4,7 @@

 import type { ToolCallContext } from "@oh-my-pi/pi-agent-core";
 import type { RenderResultOptions } from "@oh-my-pi/pi-coding-agent/extensibility/custom-tools/types";
-import type { FileDiagnosticsResult } from "@oh-my-pi/pi-coding-agent/lsp/index";
+import type { FileDiagnosticsResult } from "@oh-my-pi/pi-coding-agent/lsp";
 import { renderDiff as renderDiffColored } from "@oh-my-pi/pi-coding-agent/modes/components/diff";
 import { getLanguageFromPath, type Theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import type { OutputMeta } from "@oh-my-pi/pi-coding-agent/tools/output-meta";
@@ -32,7 +32,7 @@ import { join } from "node:path";
 import { Agent, type AgentEvent, type AgentMessage, type AgentTool, type ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import { type Message, type Model, supportsXhigh } from "@oh-my-pi/pi-ai";
 // Import discovery to register all providers on startup
-import { loadCapability } from "@oh-my-pi/pi-coding-agent/capability/index";
+import { loadCapability } from "@oh-my-pi/pi-coding-agent/capability";
 import { type Rule, ruleCapability } from "@oh-my-pi/pi-coding-agent/capability/rule";
 import { getAgentDir, getConfigDirPaths } from "@oh-my-pi/pi-coding-agent/config";
 import { CursorExecHandlers } from "@oh-my-pi/pi-coding-agent/cursor";
@@ -53,7 +53,7 @@ import "./discovery";
 import {
 	type CustomCommandsLoadResult,
 	loadCustomCommands as loadCustomCommandsInternal,
-} from "./extensibility/custom-commands/index";
+} from "./extensibility/custom-commands";
 import type { CustomTool, CustomToolContext, CustomToolSessionEvent } from "./extensibility/custom-tools/types";
 import {
 	discoverAndLoadExtensions,
@@ -67,7 +67,7 @@ import {
 	loadExtensions,
 	type ToolDefinition,
 	wrapRegisteredTools,
-} from "./extensibility/extensions/index";
+} from "./extensibility/extensions";
 import { loadSkills as loadSkillsInternal, type Skill, type SkillWarning } from "./extensibility/skills";
 import { type FileSlashCommand, loadSlashCommands as loadSlashCommandsInternal } from "./extensibility/slash-commands";
 import {
@@ -77,7 +77,7 @@ import {
 	RuleProtocolHandler,
 	SkillProtocolHandler,
 } from "./internal-urls";
-import { discoverAndLoadMCPTools, type MCPManager, type MCPToolsLoadResult } from "./mcp/index";
+import { discoverAndLoadMCPTools, type MCPManager, type MCPToolsLoadResult } from "./mcp";
 import { AgentSession } from "./session/agent-session";
 import { AuthStorage } from "./session/auth-storage";
 import { convertToLlm } from "./session/messages";
@@ -88,8 +88,6 @@ import {
 	loadProjectContextFiles as loadContextFilesInternal,
 } from "./system-prompt";
 import { AgentOutputManager } from "./task/output-manager";
-import { ToolContextStore } from "./tools/context";
-import { getGeminiImageTools } from "./tools/gemini-image";
 import {
 	BashTool,
 	BUILTIN_TOOLS,
@@ -108,7 +106,9 @@ import {
 	type ToolSession,
 	WriteTool,
 	warmupLspServers,
-} from "./tools/index";
+} from "./tools";
+import { ToolContextStore } from "./tools/context";
+import { getGeminiImageTools } from "./tools/gemini-image";
 import { wrapToolsWithMetaNotice } from "./tools/output-meta";
 import { EventBus } from "./utils/event-bus";
 import { time } from "./utils/timings";
@@ -218,11 +218,11 @@ export type {
 	ExtensionContext,
 	ExtensionFactory,
 	ToolDefinition,
-} from "@oh-my-pi/pi-coding-agent/extensibility/extensions/index";
+} from "@oh-my-pi/pi-coding-agent/extensibility/extensions";
 export type { Skill } from "@oh-my-pi/pi-coding-agent/extensibility/skills";
 export type { FileSlashCommand } from "@oh-my-pi/pi-coding-agent/extensibility/slash-commands";
-export type { MCPManager, MCPServerConfig, MCPServerConnection, MCPToolsLoadResult } from "./mcp/index";
-export type { Tool } from "./tools/index";
+export type { MCPManager, MCPServerConfig, MCPServerConnection, MCPToolsLoadResult } from "./mcp";
+export type { Tool } from "./tools";

 export {
 	// Individual tool classes (for custom usage)
@@ -38,9 +38,9 @@ import {
 } from "@oh-my-pi/pi-coding-agent/config/prompt-templates";
 import type { SettingsManager, SkillsSettings } from "@oh-my-pi/pi-coding-agent/config/settings-manager";
 import { type BashResult, executeBash as executeBashCommand } from "@oh-my-pi/pi-coding-agent/exec/bash-executor";
-import { exportSessionToHtml } from "@oh-my-pi/pi-coding-agent/export/html/index";
+import { exportSessionToHtml } from "@oh-my-pi/pi-coding-agent/export/html";
 import type { TtsrManager } from "@oh-my-pi/pi-coding-agent/export/ttsr";
-import type { LoadedCustomCommand } from "@oh-my-pi/pi-coding-agent/extensibility/custom-commands/index";
+import type { LoadedCustomCommand } from "@oh-my-pi/pi-coding-agent/extensibility/custom-commands";
 import type {
 	ExtensionCommandContext,
 	ExtensionRunner,
@@ -78,7 +78,7 @@ import {
 	generateBranchSummary,
 	prepareCompaction,
 	shouldCompact,
-} from "./compaction/index";
+} from "./compaction";
 import {
 	type BashExecutionMessage,
 	type BranchSummaryMessage,
@@ -13,7 +13,7 @@ import {
 	type ContextFile,
 	loadCapability,
 	type SystemPrompt as SystemPromptFile,
-} from "@oh-my-pi/pi-coding-agent/discovery/index";
+} from "@oh-my-pi/pi-coding-agent/discovery";
 import { loadSkills, type Skill } from "@oh-my-pi/pi-coding-agent/extensibility/skills";
 import customSystemPromptTemplate from "@oh-my-pi/pi-coding-agent/prompts/system/custom-system-prompt.md" with {
 	type: "text",
@@ -21,7 +21,7 @@ import customSystemPromptTemplate from "@oh-my-pi/pi-coding-agent/prompts/system
 import systemPromptTemplate from "@oh-my-pi/pi-coding-agent/prompts/system/system-prompt.md" with { type: "text" };
 import { $ } from "bun";
 import chalk from "chalk";
-import type { ToolName } from "./tools/index";
+import type { ToolName } from "./tools";

 interface GitContext {
 	isRepo: boolean;
@@ -9,7 +9,7 @@ import type { AgentEvent, ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import type { ModelRegistry } from "@oh-my-pi/pi-coding-agent/config/model-registry";
 import { formatModelString, parseModelPattern } from "@oh-my-pi/pi-coding-agent/config/model-resolver";
 import { checkPythonKernelAvailability } from "@oh-my-pi/pi-coding-agent/ipy/kernel";
-import { LspTool } from "@oh-my-pi/pi-coding-agent/lsp/index";
+import { LspTool } from "@oh-my-pi/pi-coding-agent/lsp";
 import type { LspParams } from "@oh-my-pi/pi-coding-agent/lsp/types";
 import { callTool } from "@oh-my-pi/pi-coding-agent/mcp/client";
 import type { MCPManager } from "@oh-my-pi/pi-coding-agent/mcp/manager";
@@ -24,7 +24,7 @@ import { renderStatusLine } from "@oh-my-pi/pi-coding-agent/tui";
 import type { Component } from "@oh-my-pi/pi-tui";
 import { Text } from "@oh-my-pi/pi-tui";
 import { Type } from "@sinclair/typebox";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { ToolUIKit } from "./render-utils";

 // =============================================================================
@@ -12,9 +12,8 @@ import { renderOutputBlock, renderStatusLine } from "@oh-my-pi/pi-coding-agent/t
 import type { Component } from "@oh-my-pi/pi-tui";
 import { Text } from "@oh-my-pi/pi-tui";
 import { Type } from "@sinclair/typebox";
-
+import type { ToolSession } from ".";
 import { checkBashInterception, checkSimpleLsInterception } from "./bash-interceptor";
-import type { ToolSession } from "./index";
 import { allocateOutputArtifact, createTailBuffer } from "./output-utils";
 import { resolveToCwd } from "./path-utils";
 import { formatBytes, wrapBrackets } from "./render-utils";
@@ -8,7 +8,7 @@ import type { Component } from "@oh-my-pi/pi-tui";
 import { Text } from "@oh-my-pi/pi-tui";
 import { untilAborted } from "@oh-my-pi/pi-utils";
 import { Type } from "@sinclair/typebox";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import {
 	formatCount,
 	formatEmptyMessage,
@@ -10,7 +10,7 @@ import { subprocessToolRegistry } from "@oh-my-pi/pi-coding-agent/task/subproces
 import type { Static, TObject } from "@sinclair/typebox";
 import { Type } from "@sinclair/typebox";
 import Ajv, { type ErrorObject, type ValidateFunction } from "ajv";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { jtdToJsonSchema } from "./jtd-to-json-schema";

 export interface CompleteDetails {
@@ -9,7 +9,7 @@ import type { OutputMeta } from "@oh-my-pi/pi-coding-agent/tools/output-meta";
 import { ToolAbortError } from "@oh-my-pi/pi-coding-agent/tools/tool-errors";
 import { renderOutputBlock, renderStatusLine } from "@oh-my-pi/pi-coding-agent/tui";
 import { ensureTool } from "@oh-my-pi/pi-coding-agent/utils/tools-manager";
-import { specialHandlers } from "@oh-my-pi/pi-coding-agent/web/scrapers/index";
+import { specialHandlers } from "@oh-my-pi/pi-coding-agent/web/scrapers";
 import type { RenderResult } from "@oh-my-pi/pi-coding-agent/web/scrapers/types";
 import { finalizeOutput, loadPage, MAX_OUTPUT_CHARS } from "@oh-my-pi/pi-coding-agent/web/scrapers/types";
 import { convertWithMarkitdown, fetchBinary } from "@oh-my-pi/pi-coding-agent/web/scrapers/utils";
@@ -19,7 +19,7 @@ import { ptree } from "@oh-my-pi/pi-utils";
 import { type Static, Type } from "@sinclair/typebox";
 import { nanoid } from "nanoid";
 import { parse as parseHtml } from "node-html-parser";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { applyListLimit } from "./list-limit";
 import { formatExpandHint } from "./render-utils";
 import { toolResult } from "./tool-result";
@@ -15,7 +15,7 @@ import { ptree, untilAborted } from "@oh-my-pi/pi-utils";
 import type { Static } from "@sinclair/typebox";
 import { Type } from "@sinclair/typebox";

-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { applyListLimit } from "./list-limit";
 import { resolveToCwd } from "./path-utils";
 import { formatCount, formatEmptyMessage, formatErrorMessage, PREVIEW_LIMITS } from "./render-utils";
@@ -15,7 +15,7 @@ import { Text } from "@oh-my-pi/pi-tui";
 import { ptree, readLines } from "@oh-my-pi/pi-utils";
 import { Type } from "@sinclair/typebox";
 import { $ } from "bun";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { applyListLimit } from "./list-limit";
 import { resolveToCwd } from "./path-utils";
 import { formatCount, formatEmptyMessage, formatErrorMessage, PREVIEW_LIMITS } from "./render-utils";
@@ -1,5 +1,5 @@
 // Exa MCP tools (22 tools)
-export { exaTools } from "@oh-my-pi/pi-coding-agent/exa/index";
+export { exaTools } from "@oh-my-pi/pi-coding-agent/exa";
 export type { ExaRenderDetails, ExaSearchResponse, ExaSearchResult } from "@oh-my-pi/pi-coding-agent/exa/types";
 export {
 	type FileDiagnosticsResult,
@@ -11,9 +11,9 @@ export {
 	type LspWarmupOptions,
 	type LspWarmupResult,
 	warmupLspServers,
-} from "@oh-my-pi/pi-coding-agent/lsp/index";
+} from "@oh-my-pi/pi-coding-agent/lsp";
 export { EditTool, type EditToolDetails } from "@oh-my-pi/pi-coding-agent/patch";
-export { BUNDLED_AGENTS, TaskTool } from "@oh-my-pi/pi-coding-agent/task/index";
+export { BUNDLED_AGENTS, TaskTool } from "@oh-my-pi/pi-coding-agent/task";
 export {
 	companyWebSearchTools,
 	exaWebSearchTools,
@@ -31,7 +31,7 @@ export {
 	webSearchCustomTool,
 	webSearchDeepTool,
 	webSearchLinkedinTool,
-} from "@oh-my-pi/pi-coding-agent/web/search/index";
+} from "@oh-my-pi/pi-coding-agent/web/search";
 export { AskTool, type AskToolDetails } from "./ask";
 export { BashTool, type BashToolDetails, type BashToolOptions } from "./bash";
 export { CalculatorTool, type CalculatorToolDetails } from "./calculator";
@@ -64,13 +64,13 @@ import type { BashInterceptorRule } from "@oh-my-pi/pi-coding-agent/config/setti
 import type { InternalUrlRouter } from "@oh-my-pi/pi-coding-agent/internal-urls";
 import { getPreludeDocs, warmPythonEnvironment } from "@oh-my-pi/pi-coding-agent/ipy/executor";
 import { checkPythonKernelAvailability } from "@oh-my-pi/pi-coding-agent/ipy/kernel";
-import { LspTool } from "@oh-my-pi/pi-coding-agent/lsp/index";
+import { LspTool } from "@oh-my-pi/pi-coding-agent/lsp";
 import { EditTool } from "@oh-my-pi/pi-coding-agent/patch";
 import type { ArtifactManager } from "@oh-my-pi/pi-coding-agent/session/artifacts";
-import { TaskTool } from "@oh-my-pi/pi-coding-agent/task/index";
+import { TaskTool } from "@oh-my-pi/pi-coding-agent/task";
 import type { AgentOutputManager } from "@oh-my-pi/pi-coding-agent/task/output-manager";
 import type { EventBus } from "@oh-my-pi/pi-coding-agent/utils/event-bus";
-import { WebSearchTool } from "@oh-my-pi/pi-coding-agent/web/search/index";
+import { WebSearchTool } from "@oh-my-pi/pi-coding-agent/web/search";
 import { logger } from "@oh-my-pi/pi-utils";
 import { AskTool } from "./ask";
 import { BashTool } from "./bash";
@@ -8,7 +8,7 @@ import { renderFileList, renderStatusLine } from "@oh-my-pi/pi-coding-agent/tui"
 import { type Component, Text } from "@oh-my-pi/pi-tui";
 import { untilAborted } from "@oh-my-pi/pi-utils";
 import { Type } from "@sinclair/typebox";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { applyListLimit } from "./list-limit";
 import { resolveToCwd } from "./path-utils";
 import {
@@ -1,5 +1,5 @@
 import { ArtifactManager } from "@oh-my-pi/pi-coding-agent/session/artifacts";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";

 export interface TailBuffer {
 	append(chunk: string): void;
@@ -15,7 +15,7 @@ import { getTreeBranch, getTreeContinuePrefix, renderCodeCell } from "@oh-my-pi/
 import type { Component } from "@oh-my-pi/pi-tui";
 import { Text, truncateToWidth } from "@oh-my-pi/pi-tui";
 import { type Static, Type } from "@sinclair/typebox";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { allocateOutputArtifact, createTailBuffer } from "./output-utils";
 import { resolveToCwd } from "./path-utils";
 import { shortenPath, ToolUIKit, truncate } from "./render-utils";
@@ -2,7 +2,7 @@ import type { AgentTool, AgentToolContext, AgentToolResult, AgentToolUpdateCallb
 import type { SSHHost } from "@oh-my-pi/pi-coding-agent/capability/ssh";
 import { sshCapability } from "@oh-my-pi/pi-coding-agent/capability/ssh";
 import { renderPromptTemplate } from "@oh-my-pi/pi-coding-agent/config/prompt-templates";
-import { loadCapability } from "@oh-my-pi/pi-coding-agent/discovery/index";
+import { loadCapability } from "@oh-my-pi/pi-coding-agent/discovery";
 import type { RenderResultOptions } from "@oh-my-pi/pi-coding-agent/extensibility/custom-tools/types";
 import type { Theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import sshDescriptionBase from "@oh-my-pi/pi-coding-agent/prompts/tools/ssh.md" with { type: "text" };
@@ -15,7 +15,7 @@ import { renderOutputBlock, renderStatusLine } from "@oh-my-pi/pi-coding-agent/t
 import type { Component } from "@oh-my-pi/pi-tui";
 import { Text } from "@oh-my-pi/pi-tui";
 import { Type } from "@sinclair/typebox";
-import type { ToolSession } from "./index";
+import type { ToolSession } from ".";
 import { allocateOutputArtifact, createTailBuffer } from "./output-utils";
 import { formatBytes, wrapBrackets } from "./render-utils";
 import { toolResult } from "./tool-result";
@@ -12,7 +12,7 @@ import {
 	type FileDiagnosticsResult,
 	type WritethroughCallback,
 	writethroughNoop,
-} from "@oh-my-pi/pi-coding-agent/lsp/index";
+} from "@oh-my-pi/pi-coding-agent/lsp";
 import { getLanguageFromPath, type Theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import writeDescription from "@oh-my-pi/pi-coding-agent/prompts/tools/write.md" with { type: "text" };
 import type { ToolSession } from "@oh-my-pi/pi-coding-agent/sdk";
@@ -21,8 +21,15 @@ export function renderOutputBlock(options: OutputBlockOptions, theme: Theme): st
 	const v = theme.boxSharp.vertical;
 	const cap = h.repeat(3);
 	const lineWidth = Math.max(0, width);
-	const borderColor =
-		state === "error" ? "error" : state === "success" ? "success" : state === "warning" ? "warning" : "dim";
+	// Border colors: running/pending use accent, success uses dim (gray), error/warning keep their colors
+	const borderColor: "error" | "warning" | "accent" | "dim" =
+		state === "error"
+			? "error"
+			: state === "warning"
+				? "warning"
+				: state === "running" || state === "pending"
+					? "accent"
+					: "dim";
 	const border = (text: string) => theme.fg(borderColor, text);
 	const bgFn = state ? (text: string) => theme.bg(getStateBgColor(state), text) : undefined;

@@ -40,7 +40,7 @@ export function getStateIcon(icon: IconType, theme: Theme, spinnerFrame?: number
 	if (icon === "error") return theme.styledSymbol("status.error", "error");
 	if (icon === "warning") return theme.styledSymbol("status.warning", "warning");
 	if (icon === "info") return theme.styledSymbol("status.info", "accent");
-	if (icon === "pending") return theme.styledSymbol("status.pending", "muted");
+	if (icon === "pending") return theme.styledSymbol("status.pending", "accent");
 	if (spinnerFrame !== undefined) {
 		const frames = theme.spinnerFrames;
 		return frames[spinnerFrame % frames.length];
@@ -31,7 +31,7 @@ import type {
 import type { Theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import webSearchSystemPrompt from "@oh-my-pi/pi-coding-agent/prompts/system/web-search.md" with { type: "text" };
 import webSearchDescription from "@oh-my-pi/pi-coding-agent/prompts/tools/web-search.md" with { type: "text" };
-import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { formatAge } from "@oh-my-pi/pi-coding-agent/tools/render-utils";
 import { Type } from "@sinclair/typebox";
 import { findAnthropicAuth } from "./auth";
@@ -18,7 +18,7 @@ import { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manag
 import { AgentSession } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import { AuthStorage } from "@oh-my-pi/pi-coding-agent/session/auth-storage";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
-import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { nanoid } from "nanoid";
 import { API_KEY } from "./utilities";

@@ -18,7 +18,7 @@ import { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manag
 import { AgentSession, type AgentSessionEvent } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import { AuthStorage } from "@oh-my-pi/pi-coding-agent/session/auth-storage";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
-import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { nanoid } from "nanoid";
 import { API_KEY } from "./utilities";

@@ -4,7 +4,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { processFileArguments } from "@oh-my-pi/pi-coding-agent/cli/file-processor";
 import { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manager";
-import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import type { ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { ReadTool } from "@oh-my-pi/pi-coding-agent/tools/read";

 // 1x1 red PNG image as base64 (smallest valid PNG)
@@ -7,7 +7,7 @@ import type {
 	HookAPI,
 	SessionBeforeCompactEvent,
 	SessionCompactEvent,
-} from "@oh-my-pi/pi-coding-agent/extensibility/hooks/index";
+} from "@oh-my-pi/pi-coding-agent/extensibility/hooks";

 describe("Documentation example", () => {
 	it("custom compaction example should type-check correctly", () => {
@@ -16,12 +16,12 @@ import {
 	type SessionBeforeCompactEvent,
 	type SessionCompactEvent,
 	type SessionEvent,
-} from "@oh-my-pi/pi-coding-agent/extensibility/hooks/index";
+} from "@oh-my-pi/pi-coding-agent/extensibility/hooks";
 import { theme } from "@oh-my-pi/pi-coding-agent/modes/theme/theme";
 import { AgentSession } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import { AuthStorage } from "@oh-my-pi/pi-coding-agent/session/auth-storage";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
-import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { nanoid } from "nanoid";

 const API_KEY = process.env.ANTHROPIC_OAUTH_TOKEN || process.env.ANTHROPIC_API_KEY;
@@ -19,7 +19,7 @@ import { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manag
 import { AgentSession } from "@oh-my-pi/pi-coding-agent/session/agent-session";
 import { AuthStorage } from "@oh-my-pi/pi-coding-agent/session/auth-storage";
 import { SessionManager } from "@oh-my-pi/pi-coding-agent/session/session-manager";
-import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { nanoid } from "nanoid";
 import { API_KEY } from "./utilities";

@@ -13,7 +13,7 @@ import {
 	getLastAssistantUsage,
 	prepareCompaction,
 	shouldCompact,
-} from "@oh-my-pi/pi-coding-agent/session/compaction/index";
+} from "@oh-my-pi/pi-coding-agent/session/compaction";
 import {
 	buildSessionContext,
 	type CompactionEntry,
@@ -4,7 +4,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import * as pythonExecutor from "@oh-my-pi/pi-coding-agent/ipy/executor";
 import * as pythonKernel from "@oh-my-pi/pi-coding-agent/ipy/kernel";
-import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools/index";
+import { createTools, type ToolSession } from "@oh-my-pi/pi-coding-agent/tools";
 import { PythonTool } from "@oh-my-pi/pi-coding-agent/tools/python";

 function createSettings(overrides?: Partial<ToolSession["settings"]>): ToolSession["settings"] {
@@ -1,9 +1,8 @@
 import { afterEach, beforeEach, describe, expect, it } from "bun:test";
 import { existsSync, mkdirSync, rmSync } from "node:fs";
 import { join } from "node:path";
-import { getAgentDbPath } from "@oh-my-pi/pi-coding-agent/config";
 import { SettingsManager } from "@oh-my-pi/pi-coding-agent/config/settings-manager";
-import { AgentStorage } from "@oh-my-pi/pi-coding-agent/session/agent-storage";
+import { YAML } from "bun";

 describe("SettingsManager", () => {
 	let testDir: string;
@@ -23,6 +22,21 @@ describe("SettingsManager", () => {
 		mkdirSync(join(projectDir, ".pi"), { recursive: true });
 	});

+	const getConfigPath = () => join(agentDir, "config.yml");
+
+	const writeSettings = async (settings: Record<string, unknown>) => {
+		await Bun.write(getConfigPath(), YAML.stringify(settings, null, 2));
+	};
+
+	const readSettings = async (): Promise<Record<string, unknown>> => {
+		const file = Bun.file(getConfigPath());
+		if (!(await file.exists())) return {};
+		const content = await file.text();
+		const parsed = YAML.parse(content);
+		if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) return {};
+		return parsed as Record<string, unknown>;
+	};
+
 	afterEach(() => {
 		if (existsSync(testDir)) {
 			rmSync(testDir, { recursive: true });
@@ -33,9 +47,8 @@ describe("SettingsManager", () => {
 	// This ensures external edits (via AgentStorage directly) aren't lost when the app saves.
 	describe("preserves externally added settings", () => {
 		it("should preserve enabledModels when changing thinking level", async () => {
-			// Seed initial settings in DB
-			const storage = await AgentStorage.open(getAgentDbPath(agentDir));
-			storage.saveSettings({
+			// Seed initial settings in config.yml
+			await writeSettings({
 				theme: "dark",
 				modelRoles: { default: "claude-sonnet" },
 			});
@@ -44,60 +57,58 @@ describe("SettingsManager", () => {
 			const manager = await SettingsManager.create(projectDir, agentDir);

 			// Simulate external edit (e.g., user modifying DB directly or another process)
-			storage.saveSettings({
+			await writeSettings({
 				theme: "dark",
 				modelRoles: { default: "claude-sonnet" },
 				enabledModels: ["claude-opus-4-5", "gpt-5.2-codex"],
 			});

 			// Manager saves a change - should merge, not overwrite
-			manager.setDefaultThinkingLevel("high");
+			await manager.setDefaultThinkingLevel("high");

-			const savedSettings = storage.getSettings() ?? {};
+			const savedSettings = await readSettings();
 			expect(savedSettings.enabledModels).toEqual(["claude-opus-4-5", "gpt-5.2-codex"]);
 			expect(savedSettings.defaultThinkingLevel).toBe("high");
 			expect(savedSettings.theme).toBe("dark");
-			expect(savedSettings.modelRoles?.default).toBe("claude-sonnet");
+			expect((savedSettings.modelRoles as { default?: string } | undefined)?.default).toBe("claude-sonnet");
 		});

 		it("should preserve custom settings when changing theme", async () => {
-			const storage = await AgentStorage.open(getAgentDbPath(agentDir));
-			storage.saveSettings({
+			await writeSettings({
 				modelRoles: { default: "claude-sonnet" },
 			});

 			const manager = await SettingsManager.create(projectDir, agentDir);

-			storage.saveSettings({
+			await writeSettings({
 				modelRoles: { default: "claude-sonnet" },
 				shellPath: "/bin/zsh",
 				extensions: ["/path/to/extension.ts"],
 			});

-			manager.setTheme("light");
+			await manager.setTheme("light");

-			const savedSettings = storage.getSettings() ?? {};
+			const savedSettings = await readSettings();
 			expect(savedSettings.shellPath).toBe("/bin/zsh");
 			expect(savedSettings.extensions).toEqual(["/path/to/extension.ts"]);
 			expect(savedSettings.theme).toBe("light");
 		});

 		it("should let in-memory changes override file changes for same key", async () => {
-			const storage = await AgentStorage.open(getAgentDbPath(agentDir));
-			storage.saveSettings({
+			await writeSettings({
 				theme: "dark",
 			});

 			const manager = await SettingsManager.create(projectDir, agentDir);

-			storage.saveSettings({
+			await writeSettings({
 				theme: "dark",
 				defaultThinkingLevel: "low",
 			});

-			manager.setDefaultThinkingLevel("high");
+			await manager.setDefaultThinkingLevel("high");

-			const savedSettings = storage.getSettings() ?? {};
+			const savedSettings = await readSettings();
 			expect(savedSettings.defaultThinkingLevel).toBe("high");
 		});
 	});
--- a/Show More
+++ b/Show More