@oh-my-pi/pi-coding-agent 1.341.0 → 2.1.1337

package/src/core/logger.ts

@@ -0,0 +1,112 @@
+/**
+ * Centralized file logger for pi.
+ *
+ * Logs to ~/.pi/logs/ with size-based rotation, supporting concurrent pi instances.
+ * Each log entry includes process.pid for traceability.
+ */
+
+import { existsSync, mkdirSync } from "node:fs";
+import { homedir } from "node:os";
+import { join } from "node:path";
+import winston from "winston";
+import DailyRotateFile from "winston-daily-rotate-file";
+import { CONFIG_DIR_NAME } from "../config";
+
+/** Get the logs directory (~/.pi/logs/) */
+function getLogsDir(): string {
+	return join(homedir(), CONFIG_DIR_NAME, "logs");
+}
+
+/** Ensure logs directory exists */
+function ensureLogsDir(): string {
+	const logsDir = getLogsDir();
+	if (!existsSync(logsDir)) {
+		mkdirSync(logsDir, { recursive: true });
+	}
+	return logsDir;
+}
+
+/** Custom format that includes pid and flattens metadata */
+const logFormat = winston.format.combine(
+	winston.format.timestamp({ format: "YYYY-MM-DDTHH:mm:ss.SSSZ" }),
+	winston.format.printf(({ timestamp, level, message, ...meta }) => {
+		const entry: Record<string, unknown> = {
+			timestamp,
+			level,
+			pid: process.pid,
+			message,
+		};
+		// Flatten metadata into entry
+		for (const [key, value] of Object.entries(meta)) {
+			if (key !== "level" && key !== "timestamp" && key !== "message") {
+				entry[key] = value;
+			}
+		}
+		return JSON.stringify(entry);
+	}),
+);
+
+/** Size-based rotating file transport */
+const fileTransport = new DailyRotateFile({
+	dirname: ensureLogsDir(),
+	filename: "pi.%DATE%.log",
+	datePattern: "YYYY-MM-DD",
+	maxSize: "10m",
+	maxFiles: 5,
+	zippedArchive: true,
+});
+
+/** The winston logger instance */
+const winstonLogger = winston.createLogger({
+	level: "debug",
+	format: logFormat,
+	transports: [fileTransport],
+	// Don't exit on error - logging failures shouldn't crash the app
+	exitOnError: false,
+});
+
+/** Logger type exposed to plugins and internal code */
+export interface Logger {
+	error(message: string, context?: Record<string, unknown>): void;
+	warn(message: string, context?: Record<string, unknown>): void;
+	debug(message: string, context?: Record<string, unknown>): void;
+}
+
+/**
+ * Centralized logger for pi.
+ *
+ * Logs to ~/.pi/logs/pi.YYYY-MM-DD.log with size-based rotation.
+ * Safe for concurrent access from multiple pi instances.
+ *
+ * @example
+ * ```typescript
+ * import { logger } from "../core/logger";
+ *
+ * logger.error("MCP request failed", { url, method });
+ * logger.warn("Theme file invalid, using fallback", { path });
+ * logger.debug("LSP fallback triggered", { reason });
+ * ```
+ */
+export const logger: Logger = {
+	error(message: string, context?: Record<string, unknown>): void {
+		try {
+			winstonLogger.error(message, context);
+		} catch {
+			// Silently ignore logging failures
+		}
+	},
+	warn(message: string, context?: Record<string, unknown>): void {
+		try {
+			winstonLogger.warn(message, context);
+		} catch {
+			// Silently ignore logging failures
+		}
+	},
+	debug(message: string, context?: Record<string, unknown>): void {
+		try {
+			winstonLogger.debug(message, context);
+		} catch {
+			// Silently ignore logging failures
+		}
+	},
+};

package/src/core/mcp/client.ts

@@ -4,8 +4,8 @@
  * Handles connection initialization, tool listing, and tool calling.
  */
 
-import { createHttpTransport } from "./transports/http.js";
-import { createStdioTransport } from "./transports/stdio.js";
+import { createHttpTransport } from "./transports/http";
+import { createStdioTransport } from "./transports/stdio";
 import type {
 	MCPHttpServerConfig,
 	MCPInitializeParams,
@@ -20,7 +20,7 @@ import type {
 	MCPToolDefinition,
 	MCPToolsListResult,
 	MCPTransport,
-} from "./types.js";
+} from "./types";
 
 /** MCP protocol version we support */
 const PROTOCOL_VERSION = "2025-03-26";

package/src/core/mcp/config.ts

@@ -8,7 +8,7 @@
 import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { join } from "node:path";
-import type { MCPConfigFile, MCPServerConfig } from "./types.js";
+import type { MCPConfigFile, MCPServerConfig } from "./types";
 
 /** Environment variable expansion pattern: ${VAR} or ${VAR:-default} */
 const ENV_VAR_PATTERN = /\$\{([^}:]+)(?::-([^}]*))?\}/g;

package/src/core/mcp/index.ts

@@ -6,10 +6,10 @@
  */
 
 // Client
-export { callTool, connectToServer, disconnectServer, listTools, serverSupportsTools } from "./client.js";
+export { callTool, connectToServer, disconnectServer, listTools, serverSupportsTools } from "./client";
 
 // Config
-export type { ExaFilterResult, LoadMCPConfigsOptions, LoadMCPConfigsResult } from "./config.js";
+export type { ExaFilterResult, LoadMCPConfigsOptions, LoadMCPConfigsResult } from "./config";
 export {
 	expandEnvVars,
 	extractExaApiKey,
@@ -20,19 +20,19 @@ export {
 	loadMCPConfigFile,
 	mergeMCPConfigs,
 	validateServerConfig,
-} from "./config.js";
+} from "./config";
 // Loader (for SDK integration)
-export type { MCPToolsLoadOptions, MCPToolsLoadResult } from "./loader.js";
-export { discoverAndLoadMCPTools } from "./loader.js";
+export type { MCPToolsLoadOptions, MCPToolsLoadResult } from "./loader";
+export { discoverAndLoadMCPTools } from "./loader";
 // Manager
-export type { MCPDiscoverOptions, MCPLoadResult } from "./manager.js";
-export { createMCPManager, MCPManager } from "./manager.js";
+export type { MCPDiscoverOptions, MCPLoadResult } from "./manager";
+export { createMCPManager, MCPManager } from "./manager";
 // Tool bridge
-export type { MCPToolDetails } from "./tool-bridge.js";
-export { createMCPTool, createMCPToolName, createMCPTools, parseMCPToolName } from "./tool-bridge.js";
+export type { MCPToolDetails } from "./tool-bridge";
+export { createMCPTool, createMCPToolName, createMCPTools, parseMCPToolName } from "./tool-bridge";
 // Transports
-export { createHttpTransport, HttpTransport } from "./transports/http.js";
-export { createStdioTransport, StdioTransport } from "./transports/stdio.js";
+export { createHttpTransport, HttpTransport } from "./transports/http";
+export { createStdioTransport, StdioTransport } from "./transports/stdio";
 // Types
 export type {
 	MCPConfigFile,
@@ -46,4 +46,4 @@ export type {
 	MCPToolDefinition,
 	MCPToolWithServer,
 	MCPTransport,
-} from "./types.js";
+} from "./types";

package/src/core/mcp/loader.ts

@@ -4,8 +4,8 @@
  * Integrates MCP tool discovery with the custom tools system.
  */
 
-import type { LoadedCustomTool } from "../custom-tools/types.js";
-import { type MCPLoadResult, MCPManager } from "./manager.js";
+import type { LoadedCustomTool } from "../custom-tools/types";
+import { type MCPLoadResult, MCPManager } from "./manager";
 
 /** Result from loading MCP tools */
 export interface MCPToolsLoadResult {

package/src/core/mcp/manager.ts

@@ -6,12 +6,12 @@
  */
 
 import type { TSchema } from "@sinclair/typebox";
-import type { CustomTool } from "../custom-tools/types.js";
-import { connectToServer, disconnectServer, listTools } from "./client.js";
-import { type LoadMCPConfigsOptions, loadAllMCPConfigs, validateServerConfig } from "./config.js";
-import type { MCPToolDetails } from "./tool-bridge.js";
-import { createMCPTools } from "./tool-bridge.js";
-import type { MCPServerConfig, MCPServerConnection } from "./types.js";
+import type { CustomTool } from "../custom-tools/types";
+import { connectToServer, disconnectServer, listTools } from "./client";
+import { type LoadMCPConfigsOptions, loadAllMCPConfigs, validateServerConfig } from "./config";
+import type { MCPToolDetails } from "./tool-bridge";
+import { createMCPTools } from "./tool-bridge";
+import type { MCPServerConfig, MCPServerConnection } from "./types";
 
 /** Result of loading MCP tools */
 export interface MCPLoadResult {

package/src/core/mcp/tool-bridge.ts

@@ -5,9 +5,9 @@
  */
 
 import type { TSchema } from "@sinclair/typebox";
-import type { CustomTool, CustomToolResult } from "../custom-tools/types.js";
-import { callTool } from "./client.js";
-import type { MCPContent, MCPServerConnection, MCPToolDefinition } from "./types.js";
+import type { CustomTool, CustomToolResult } from "../custom-tools/types";
+import { callTool } from "./client";
+import type { MCPContent, MCPServerConnection, MCPToolDefinition } from "./types";
 
 /** Details included in MCP tool results for rendering */
 export interface MCPToolDetails {

package/src/core/mcp/transports/http.ts

@@ -5,7 +5,7 @@
  * Based on MCP spec 2025-03-26.
  */
 
-import type { JsonRpcResponse, MCPHttpServerConfig, MCPSseServerConfig, MCPTransport } from "../types.js";
+import type { JsonRpcResponse, MCPHttpServerConfig, MCPSseServerConfig, MCPTransport } from "../types";
 
 /** Generate unique request ID */
 function generateId(): string {

package/src/core/mcp/transports/index.ts

@@ -2,5 +2,5 @@
  * MCP transport exports.
  */
 
-export { createHttpTransport, HttpTransport } from "./http.js";
-export { createStdioTransport, StdioTransport } from "./stdio.js";
+export { createHttpTransport, HttpTransport } from "./http";
+export { createStdioTransport, StdioTransport } from "./stdio";

package/src/core/mcp/transports/stdio.ts

@@ -6,7 +6,7 @@
  */
 
 import { type Subprocess, spawn } from "bun";
-import type { JsonRpcResponse, MCPStdioServerConfig, MCPTransport } from "../types.js";
+import type { JsonRpcResponse, MCPStdioServerConfig, MCPTransport } from "../types";
 
 /** Generate unique request ID */
 function generateId(): string {

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,
 	});