@oh-my-pi/pi-coding-agent 1.341.0 → 2.0.1337

package/src/core/messages.ts

@@ -64,6 +64,19 @@ export interface CompactionSummaryMessage {
 	timestamp: number;
 }
 
+/**
+ * Message type for auto-read file mentions via @filepath syntax.
+ */
+export interface FileMentionMessage {
+	role: "fileMention";
+	files: Array<{
+		path: string;
+		content: string;
+		lineCount: number;
+	}>;
+	timestamp: number;
+}
+
 // Extend CustomAgentMessages via declaration merging
 declare module "@oh-my-pi/pi-agent-core" {
 	interface CustomAgentMessages {
@@ -71,6 +84,7 @@ declare module "@oh-my-pi/pi-agent-core" {
 		hookMessage: HookMessage;
 		branchSummary: BranchSummaryMessage;
 		compactionSummary: CompactionSummaryMessage;
+		fileMention: FileMentionMessage;
 	}
 }
 
@@ -175,6 +189,14 @@ export function convertToLlm(messages: AgentMessage[]): Message[] {
 						],
 						timestamp: m.timestamp,
 					};
+				case "fileMention": {
+					const fileContents = m.files.map((f) => `<file path="${f.path}">\n${f.content}\n</file>`).join("\n\n");
+					return {
+						role: "user",
+						content: [{ type: "text" as const, text: `<system-reminder>\n${fileContents}\n</system-reminder>` }],
+						timestamp: m.timestamp,
+					};
+				}
 				case "user":
 				case "assistant":
 				case "toolResult":

package/src/core/model-registry.ts

@@ -2,6 +2,7 @@
  * Model registry - manages built-in and custom models, provides API key resolution.
  */
 
+import { existsSync, readFileSync } from "node:fs";
 import {
 	type Api,
 	getGitHubCopilotBaseUrl,
@@ -13,8 +14,7 @@ import {
 } from "@oh-my-pi/pi-ai";
 import { type Static, Type } from "@sinclair/typebox";
 import AjvModule from "ajv";
-import { existsSync, readFileSync } from "fs";
-import type { AuthStorage } from "./auth-storage.js";
+import type { AuthStorage } from "./auth-storage";
 
 const Ajv = (AjvModule as any).default || AjvModule;
 

package/src/core/model-resolver.ts

@@ -6,8 +6,8 @@ import type { ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import { type Api, type KnownProvider, type Model, modelsAreEqual } from "@oh-my-pi/pi-ai";
 import chalk from "chalk";
 import { minimatch } from "minimatch";
-import { isValidThinkingLevel } from "../cli/args.js";
-import type { ModelRegistry } from "./model-registry.js";
+import { isValidThinkingLevel } from "../cli/args";
+import type { ModelRegistry } from "./model-registry";
 
 /** Default model IDs for each known provider */
 export const defaultModelPerProvider: Record<KnownProvider, string> = {

package/src/core/plugins/doctor.ts

@@ -1,4 +1,4 @@
-import type { DoctorCheck } from "./types.js";
+import type { DoctorCheck } from "./types";
 
 export async function runDoctorChecks(): Promise<DoctorCheck[]> {
 	const checks: DoctorCheck[] = [];

package/src/core/plugins/index.ts

@@ -1,5 +1,5 @@
 // Plugin system exports
-export { formatDoctorResults, runDoctorChecks } from "./doctor.js";
+export { formatDoctorResults, runDoctorChecks } from "./doctor";
 export {
 	getAllPluginCommandPaths,
 	getAllPluginHookPaths,
@@ -9,16 +9,16 @@ export {
 	resolvePluginCommandPaths,
 	resolvePluginHookPaths,
 	resolvePluginToolPaths,
-} from "./loader.js";
-export { PluginManager, parseSettingValue, validateSetting } from "./manager.js";
-export { extractPackageName, formatPluginSpec, parsePluginSpec } from "./parser.js";
+} from "./loader";
+export { PluginManager, parseSettingValue, validateSetting } from "./manager";
+export { extractPackageName, formatPluginSpec, parsePluginSpec } from "./parser";
 export {
 	getPluginsDir,
 	getPluginsLockfile,
 	getPluginsNodeModules,
 	getPluginsPackageJson,
 	getProjectPluginOverrides,
-} from "./paths.js";
+} from "./paths";
 export type {
 	BooleanSetting,
 	DoctorCheck,
@@ -35,4 +35,4 @@ export type {
 	PluginSettingType,
 	ProjectPluginOverrides,
 	StringSetting,
-} from "./types.js";
+} from "./types";

package/src/core/plugins/installer.ts

@@ -1,7 +1,7 @@
-import { mkdir } from "fs/promises";
-import { join, resolve } from "path";
-import { getAgentDir } from "../../config.js";
-import type { InstalledPlugin } from "./types.js";
+import { mkdir } from "node:fs/promises";
+import { join, resolve } from "node:path";
+import { getAgentDir } from "../../config";
+import type { InstalledPlugin } from "./types";
 
 const PLUGINS_DIR = join(getAgentDir(), "plugins");
 

package/src/core/plugins/loader.ts

@@ -5,15 +5,10 @@
  * based on manifest entries and enabled features.
  */
 
-import { existsSync, readFileSync } from "fs";
-import { join } from "path";
-import {
-	getPluginsLockfile,
-	getPluginsNodeModules,
-	getPluginsPackageJson,
-	getProjectPluginOverrides,
-} from "./paths.js";
-import type { InstalledPlugin, PluginManifest, PluginRuntimeConfig, ProjectPluginOverrides } from "./types.js";
+import { existsSync, readFileSync } from "node:fs";
+import { join } from "node:path";
+import { getPluginsLockfile, getPluginsNodeModules, getPluginsPackageJson, getProjectPluginOverrides } from "./paths";
+import type { InstalledPlugin, PluginManifest, PluginRuntimeConfig, ProjectPluginOverrides } from "./types";
 
 // =============================================================================
 // Runtime Config Loading

package/src/core/plugins/manager.ts

@@ -1,13 +1,13 @@
-import { existsSync, lstatSync, mkdirSync, readFileSync, symlinkSync, unlinkSync, writeFileSync } from "fs";
-import { join, resolve } from "path";
-import { extractPackageName, parsePluginSpec } from "./parser.js";
+import { existsSync, lstatSync, mkdirSync, readFileSync, symlinkSync, unlinkSync, writeFileSync } from "node:fs";
+import { join, resolve } from "node:path";
+import { extractPackageName, parsePluginSpec } from "./parser";
 import {
 	getPluginsDir,
 	getPluginsLockfile,
 	getPluginsNodeModules,
 	getPluginsPackageJson,
 	getProjectPluginOverrides,
-} from "./paths.js";
+} from "./paths";
 import type {
 	DoctorCheck,
 	DoctorOptions,
@@ -17,7 +17,7 @@ import type {
 	PluginRuntimeConfig,
 	PluginSettingSchema,
 	ProjectPluginOverrides,
-} from "./types.js";
+} from "./types";
 
 // =============================================================================
 // Validation

package/src/core/plugins/paths.ts

@@ -1,6 +1,6 @@
-import { homedir } from "os";
-import { join } from "path";
-import { CONFIG_DIR_NAME } from "../../config.js";
+import { homedir } from "node:os";
+import { join } from "node:path";
+import { CONFIG_DIR_NAME } from "../../config";
 
 // =============================================================================
 // Plugin Directory Paths

package/src/core/sdk.ts

@@ -29,34 +29,38 @@
  * ```
  */
 
+import { join } from "node:path";
 import { Agent, type ThinkingLevel } from "@oh-my-pi/pi-agent-core";
 import type { Model } from "@oh-my-pi/pi-ai";
-import { join } from "path";
-import { getAgentDir } from "../config.js";
-import { AgentSession } from "./agent-session.js";
-import { AuthStorage } from "./auth-storage.js";
+import { getAgentDir } from "../config";
+import { AgentSession } from "./agent-session";
+import { AuthStorage } from "./auth-storage";
+import {
+	type CustomCommandsLoadResult,
+	loadCustomCommands as loadCustomCommandsInternal,
+} from "./custom-commands/index";
 import {
 	type CustomToolsLoadResult,
 	discoverAndLoadCustomTools,
 	type LoadedCustomTool,
 	wrapCustomTools,
-} from "./custom-tools/index.js";
-import type { CustomTool } from "./custom-tools/types.js";
-import { discoverAndLoadHooks, HookRunner, type LoadedHook, wrapToolsWithHooks } from "./hooks/index.js";
-import type { HookFactory } from "./hooks/types.js";
-import { discoverAndLoadMCPTools, type MCPManager, type MCPToolsLoadResult } from "./mcp/index.js";
-import { convertToLlm } from "./messages.js";
-import { ModelRegistry } from "./model-registry.js";
-import { SessionManager } from "./session-manager.js";
-import { type Settings, SettingsManager, type SkillsSettings } from "./settings-manager.js";
-import { loadSkills as loadSkillsInternal, type Skill } from "./skills.js";
-import { type FileSlashCommand, loadSlashCommands as loadSlashCommandsInternal } from "./slash-commands.js";
+} from "./custom-tools/index";
+import type { CustomTool } from "./custom-tools/types";
+import { discoverAndLoadHooks, HookRunner, type LoadedHook, wrapToolsWithHooks } from "./hooks/index";
+import type { HookFactory } from "./hooks/types";
+import { discoverAndLoadMCPTools, type MCPManager, type MCPToolsLoadResult } from "./mcp/index";
+import { convertToLlm } from "./messages";
+import { ModelRegistry } from "./model-registry";
+import { SessionManager } from "./session-manager";
+import { type CommandsSettings, type Settings, SettingsManager, type SkillsSettings } from "./settings-manager";
+import { loadSkills as loadSkillsInternal, type Skill } from "./skills";
+import { type FileSlashCommand, loadSlashCommands as loadSlashCommandsInternal } from "./slash-commands";
 import {
 	buildSystemPrompt as buildSystemPromptInternal,
 	loadProjectContextFiles as loadContextFilesInternal,
-} from "./system-prompt.js";
-import { time } from "./timings.js";
-import { createToolContextStore } from "./tools/context.js";
+} from "./system-prompt";
+import { time } from "./timings";
+import { createToolContextStore } from "./tools/context";
 import {
 	allTools,
 	applyBashInterception,
@@ -80,7 +84,7 @@ import {
 	type Tool,
 	warmupLspServers,
 	writeTool,
-} from "./tools/index.js";
+} from "./tools/index";
 
 // Types
 
@@ -127,6 +131,9 @@ export interface CreateAgentSessionOptions {
 	/** Enable MCP server discovery from .mcp.json files. Default: true */
 	enableMCP?: boolean;
 
+	/** Tool names explicitly requested (enables disabled-by-default tools) */
+	explicitTools?: string[];
+
 	/** Session manager. Default: SessionManager.create(cwd) */
 	sessionManager?: SessionManager;
 
@@ -153,13 +160,14 @@ export interface CreateAgentSessionResult {
 
 // Re-exports
 
-export type { CustomTool } from "./custom-tools/types.js";
-export type { HookAPI, HookCommandContext, HookContext, HookFactory } from "./hooks/types.js";
-export type { MCPManager, MCPServerConfig, MCPServerConnection, MCPToolsLoadResult } from "./mcp/index.js";
-export type { Settings, SkillsSettings } from "./settings-manager.js";
-export type { Skill } from "./skills.js";
-export type { FileSlashCommand } from "./slash-commands.js";
-export type { Tool } from "./tools/index.js";
+export type { CustomCommand, CustomCommandFactory } from "./custom-commands/types";
+export type { CustomTool } from "./custom-tools/types";
+export type { HookAPI, HookCommandContext, HookContext, HookFactory } from "./hooks/types";
+export type { MCPManager, MCPServerConfig, MCPServerConnection, MCPToolsLoadResult } from "./mcp/index";
+export type { Settings, SkillsSettings } from "./settings-manager";
+export type { Skill } from "./skills";
+export type { FileSlashCommand } from "./slash-commands";
+export type { Tool } from "./tools/index";
 
 export {
 	// Pre-built tools (use process.cwd())
@@ -278,10 +286,29 @@ export function discoverContextFiles(cwd?: string, agentDir?: string): Array<{ p
 /**
  * Discover slash commands from cwd and agentDir.
  */
-export function discoverSlashCommands(cwd?: string, agentDir?: string): FileSlashCommand[] {
+export function discoverSlashCommands(
+	cwd?: string,
+	agentDir?: string,
+	settings?: CommandsSettings,
+): FileSlashCommand[] {
 	return loadSlashCommandsInternal({
 		cwd: cwd ?? process.cwd(),
 		agentDir: agentDir ?? getDefaultAgentDir(),
+		enableClaudeUser: settings?.enableClaudeUser,
+		enableClaudeProject: settings?.enableClaudeProject,
+	});
+}
+
+/**
+ * Discover custom commands (TypeScript slash commands) from cwd and agentDir.
+ */
+export async function discoverCustomTSCommands(cwd?: string, agentDir?: string): Promise<CustomCommandsLoadResult> {
+	const resolvedCwd = cwd ?? process.cwd();
+	const resolvedAgentDir = agentDir ?? getDefaultAgentDir();
+
+	return loadCustomCommandsInternal({
+		cwd: resolvedCwd,
+		agentDir: resolvedAgentDir,
 	});
 }
 
@@ -555,12 +582,11 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 	const contextFiles = options.contextFiles ?? discoverContextFiles(cwd, agentDir);
 	time("discoverContextFiles");
 
-	// Hook runner - created early for hooks
-	let hookRunner: HookRunner | undefined;
+	// Hook runner - always created (needed for custom command context even without hooks)
+	let loadedHooks: LoadedHook[] = [];
 	if (options.hooks !== undefined) {
 		if (options.hooks.length > 0) {
-			const loadedHooks = createLoadedHooksFromDefinitions(options.hooks);
-			hookRunner = new HookRunner(loadedHooks, cwd, sessionManager, modelRegistry);
+			loadedHooks = createLoadedHooksFromDefinitions(options.hooks);
 		}
 	} else {
 		// Discover hooks, merging with additional paths
@@ -570,10 +596,9 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		for (const { path, error } of errors) {
 			console.error(`Failed to load hook "${path}": ${error}`);
 		}
-		if (hooks.length > 0) {
-			hookRunner = new HookRunner(hooks, cwd, sessionManager, modelRegistry);
-		}
+		loadedHooks = hooks;
 	}
+	const hookRunner = new HookRunner(loadedHooks, cwd, sessionManager, modelRegistry);
 
 	const sessionContext = {
 		getSessionFile: () => sessionManager.getSessionFile() ?? null,
@@ -695,6 +720,14 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 	};
 
 	let allToolsArray: Tool[] = [...builtInTools, ...wrappedCustomTools];
+
+	// Filter out hidden tools unless explicitly requested
+	if (options.explicitTools) {
+		const explicitSet = new Set(options.explicitTools);
+		allToolsArray = allToolsArray.filter((tool) => !tool.hidden || explicitSet.has(tool.name));
+	} else {
+		allToolsArray = allToolsArray.filter((tool) => !tool.hidden);
+	}
 	time("combineTools");
 
 	// Apply bash interception to redirect common shell patterns to proper tools (if enabled)
@@ -730,9 +763,17 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		systemPrompt = options.systemPrompt(defaultPrompt);
 	}
 
-	const slashCommands = options.slashCommands ?? discoverSlashCommands(cwd, agentDir);
+	const commandsSettings = settingsManager.getCommandsSettings();
+	const slashCommands = options.slashCommands ?? discoverSlashCommands(cwd, agentDir, commandsSettings);
 	time("discoverSlashCommands");
 
+	// Discover custom commands (TypeScript slash commands)
+	const customCommandsResult = await loadCustomCommandsInternal({ cwd, agentDir });
+	time("discoverCustomCommands");
+	for (const { path, error } of customCommandsResult.errors) {
+		console.error(`Failed to load custom command "${path}": ${error}`);
+	}
+
 	agent = new Agent({
 		initialState: {
 			systemPrompt,
@@ -782,6 +823,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 		fileCommands: slashCommands,
 		hookRunner,
 		customTools: customToolsResult.tools,
+		customCommands: customCommandsResult.commands,
 		skillsSettings: settingsManager.getSkillsSettings(),
 		modelRegistry,
 	});

package/src/core/session-manager.ts

@@ -1,5 +1,3 @@
-import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
-import type { ImageContent, Message, TextContent } from "@oh-my-pi/pi-ai";
 import {
 	appendFileSync,
 	closeSync,
@@ -11,16 +9,18 @@ import {
 	readSync,
 	statSync,
 	writeFileSync,
-} from "fs";
-import { join, resolve } from "path";
-import { getAgentDir as getDefaultAgentDir } from "../config.js";
+} from "node:fs";
+import { join, resolve } from "node:path";
+import type { AgentMessage } from "@oh-my-pi/pi-agent-core";
+import type { ImageContent, Message, TextContent } from "@oh-my-pi/pi-ai";
+import { getAgentDir as getDefaultAgentDir } from "../config";
 import {
 	type BashExecutionMessage,
 	createBranchSummaryMessage,
 	createCompactionSummaryMessage,
 	createHookMessage,
 	type HookMessage,
-} from "./messages.js";
+} from "./messages";
 
 export const CURRENT_SESSION_VERSION = 2;
 

package/src/core/settings-manager.ts

@@ -1,6 +1,6 @@
-import { existsSync, mkdirSync, readFileSync, writeFileSync } from "fs";
-import { dirname, join } from "path";
-import { CONFIG_DIR_NAME, getAgentDir } from "../config.js";
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { CONFIG_DIR_NAME, getAgentDir } from "../config";
 
 export interface CompactionSettings {
 	enabled?: boolean; // default: true
@@ -30,6 +30,11 @@ export interface SkillsSettings {
 	includeSkills?: string[]; // default: [] (empty = include all; glob patterns to filter)
 }
 
+export interface CommandsSettings {
+	enableClaudeUser?: boolean; // default: true (load from ~/.claude/commands/)
+	enableClaudeProject?: boolean; // default: true (load from .claude/commands/)
+}
+
 export interface TerminalSettings {
 	showImages?: boolean; // default: true (only relevant if terminal supports images)
 }
@@ -78,6 +83,7 @@ export interface Settings {
 	hooks?: string[]; // Array of hook file paths
 	customTools?: string[]; // Array of custom tool file paths
 	skills?: SkillsSettings;
+	commands?: CommandsSettings;
 	terminal?: TerminalSettings;
 	enabledModels?: string[]; // Model patterns for cycling (same format as --models CLI flag)
 	exa?: ExaSettings;
@@ -399,6 +405,13 @@ export class SettingsManager {
 		};
 	}
 
+	getCommandsSettings(): Required<CommandsSettings> {
+		return {
+			enableClaudeUser: this.settings.commands?.enableClaudeUser ?? true,
+			enableClaudeProject: this.settings.commands?.enableClaudeProject ?? true,
+		};
+	}
+
 	getShowImages(): boolean {
 		return this.settings.terminal?.showImages ?? true;
 	}

package/src/core/skills.ts

@@ -1,9 +1,9 @@
-import { existsSync, readdirSync, readFileSync, realpathSync, statSync } from "fs";
+import { existsSync, readdirSync, readFileSync, realpathSync, statSync } from "node:fs";
+import { homedir } from "node:os";
+import { basename, dirname, join, resolve } from "node:path";
 import { minimatch } from "minimatch";
-import { homedir } from "os";
-import { basename, dirname, join, resolve } from "path";
-import { CONFIG_DIR_NAME, getAgentDir } from "../config.js";
-import type { SkillsSettings } from "./settings-manager.js";
+import { CONFIG_DIR_NAME, getAgentDir } from "../config";
+import type { SkillsSettings } from "./settings-manager";
 
 /**
  * Standard frontmatter fields per Agent Skills spec.

package/src/core/slash-commands.ts

@@ -1,6 +1,8 @@
-import { existsSync, readdirSync, readFileSync } from "fs";
-import { join, resolve } from "path";
-import { CONFIG_DIR_NAME, getCommandsDir } from "../config.js";
+import { existsSync, readdirSync, readFileSync } from "node:fs";
+import { homedir } from "node:os";
+import { join, resolve } from "node:path";
+import { CONFIG_DIR_NAME, getCommandsDir } from "../config";
+import { logger } from "./logger";
 
 /**
  * Represents a custom slash command loaded from a file
@@ -98,14 +100,12 @@ export function substituteArgs(content: string, args: string[]): string {
 	return result;
 }
 
+type CommandSource = "builtin" | "claude-user" | "claude-project" | "user" | "project";
+
 /**
  * Recursively scan a directory for .md files (and symlinks to .md files) and load them as slash commands
  */
-function loadCommandsFromDir(
-	dir: string,
-	source: "builtin" | "user" | "project",
-	subdir: string = "",
-): FileSlashCommand[] {
+function loadCommandsFromDir(dir: string, source: CommandSource, subdir: string = ""): FileSlashCommand[] {
 	const commands: FileSlashCommand[] = [];
 
 	if (!existsSync(dir)) {
@@ -129,15 +129,18 @@ function loadCommandsFromDir(
 
 					const name = entry.name.slice(0, -3); // Remove .md extension
 
-					// Build source string
-					let sourceStr: string;
-					if (source === "builtin") {
-						sourceStr = subdir ? `(builtin:${subdir})` : "(builtin)";
-					} else if (source === "user") {
-						sourceStr = subdir ? `(user:${subdir})` : "(user)";
-					} else {
-						sourceStr = subdir ? `(project:${subdir})` : "(project)";
-					}
+					// Build source string based on source type
+					const sourceLabel =
+						source === "builtin"
+							? "builtin"
+							: source === "claude-user"
+								? "claude-user"
+								: source === "claude-project"
+									? "claude-project"
+									: source === "user"
+										? "user"
+										: "project";
+					const sourceStr = subdir ? `(${sourceLabel}:${subdir})` : `(${sourceLabel})`;
 
 					// Get description from frontmatter or first non-empty line
 					let description = frontmatter.description || "";
@@ -159,13 +162,13 @@ function loadCommandsFromDir(
 						content,
 						source: sourceStr,
 					});
-				} catch (_error) {
-					// Silently skip files that can't be read
+				} catch (err) {
+					logger.debug("Failed to read slash command file", { error: String(err) });
 				}
 			}
 		}
-	} catch (_error) {
-		// Silently skip directories that can't be read
+	} catch (err) {
+		logger.debug("Failed to read slash command directory", { error: String(err) });
 	}
 
 	return commands;
@@ -176,54 +179,66 @@ export interface LoadSlashCommandsOptions {
 	cwd?: string;
 	/** Agent config directory for global commands. Default: from getCommandsDir() */
 	agentDir?: string;
+	/** Enable loading from ~/.claude/commands/. Default: true */
+	enableClaudeUser?: boolean;
+	/** Enable loading from .claude/commands/. Default: true */
+	enableClaudeProject?: boolean;
 }
 
 /**
  * Load all custom slash commands from:
  * 1. Builtin: package commands/
- * 2. Global: agentDir/commands/
- * 3. Project: cwd/{CONFIG_DIR_NAME}/commands/
+ * 2. Claude user: ~/.claude/commands/
+ * 3. Claude project: .claude/commands/
+ * 4. Pi user: agentDir/commands/
+ * 5. Pi project: cwd/{CONFIG_DIR_NAME}/commands/
+ *
+ * First occurrence wins (earlier sources have priority).
  */
 export function loadSlashCommands(options: LoadSlashCommandsOptions = {}): FileSlashCommand[] {
 	const resolvedCwd = options.cwd ?? process.cwd();
 	const resolvedAgentDir = options.agentDir ?? getCommandsDir();
+	const enableClaudeUser = options.enableClaudeUser ?? true;
+	const enableClaudeProject = options.enableClaudeProject ?? true;
 
 	const commands: FileSlashCommand[] = [];
 	const seenNames = new Set<string>();
 
-	// 1. Builtin commands (from package)
-	const builtinDir = join(import.meta.dir, "../commands");
-	if (existsSync(builtinDir)) {
-		const builtinCommands = loadCommandsFromDir(builtinDir, "builtin");
-		for (const cmd of builtinCommands) {
+	const addCommands = (newCommands: FileSlashCommand[]) => {
+		for (const cmd of newCommands) {
 			if (!seenNames.has(cmd.name)) {
 				commands.push(cmd);
 				seenNames.add(cmd.name);
 			}
 		}
+	};
+
+	// 1. Builtin commands (from package)
+	const builtinDir = join(import.meta.dir, "../commands");
+	if (existsSync(builtinDir)) {
+		addCommands(loadCommandsFromDir(builtinDir, "builtin"));
 	}
 
-	// 2. Load global commands from agentDir/commands/
-	// Note: if agentDir is provided, it should be the agent dir, not the commands dir
-	const globalCommandsDir = options.agentDir ? join(options.agentDir, "commands") : resolvedAgentDir;
-	const globalCommands = loadCommandsFromDir(globalCommandsDir, "user");
-	for (const cmd of globalCommands) {
-		if (!seenNames.has(cmd.name)) {
-			commands.push(cmd);
-			seenNames.add(cmd.name);
-		}
+	// 2. Claude user commands (~/.claude/commands/)
+	if (enableClaudeUser) {
+		const claudeUserDir = join(homedir(), ".claude", "commands");
+		addCommands(loadCommandsFromDir(claudeUserDir, "claude-user"));
 	}
 
-	// 3. Load project commands from cwd/{CONFIG_DIR_NAME}/commands/
-	const projectCommandsDir = resolve(resolvedCwd, CONFIG_DIR_NAME, "commands");
-	const projectCommands = loadCommandsFromDir(projectCommandsDir, "project");
-	for (const cmd of projectCommands) {
-		if (!seenNames.has(cmd.name)) {
-			commands.push(cmd);
-			seenNames.add(cmd.name);
-		}
+	// 3. Claude project commands (.claude/commands/)
+	if (enableClaudeProject) {
+		const claudeProjectDir = resolve(resolvedCwd, ".claude", "commands");
+		addCommands(loadCommandsFromDir(claudeProjectDir, "claude-project"));
 	}
 
+	// 4. Pi user commands (agentDir/commands/)
+	const globalCommandsDir = options.agentDir ? join(options.agentDir, "commands") : resolvedAgentDir;
+	addCommands(loadCommandsFromDir(globalCommandsDir, "user"));
+
+	// 5. Pi project commands (cwd/{CONFIG_DIR_NAME}/commands/)
+	const projectCommandsDir = resolve(resolvedCwd, CONFIG_DIR_NAME, "commands");
+	addCommands(loadCommandsFromDir(projectCommandsDir, "project"));
+
 	return commands;
 }
 

package/src/core/system-prompt.ts

@@ -2,13 +2,13 @@
  * System prompt construction and project context loading
  */
 
+import { existsSync, readFileSync } from "node:fs";
+import { join, resolve } from "node:path";
 import chalk from "chalk";
-import { existsSync, readFileSync } from "fs";
-import { join, resolve } from "path";
-import { getAgentDir, getDocsPath, getExamplesPath, getReadmePath } from "../config.js";
-import type { SkillsSettings } from "./settings-manager.js";
-import { formatSkillsForPrompt, loadSkills, type Skill } from "./skills.js";
-import type { ToolName } from "./tools/index.js";
+import { getAgentDir, getDocsPath, getExamplesPath, getReadmePath } from "../config";
+import type { SkillsSettings } from "./settings-manager";
+import { formatSkillsForPrompt, loadSkills, type Skill } from "./skills";
+import type { ToolName } from "./tools/index";
 
 /**
  * Execute a git command synchronously and return stdout or null on failure.