fix(coding-agent): preserve extension tools with defaults

packages/coding-agent/CHANGELOG.md

@@ -7,7 +7,7 @@
 - Added fullscreen transcript search with `Ctrl+Shift+F`, incremental match highlighting, configurable search match theme colors, and next/previous navigation with `Enter`/`Ctrl+G` and `Shift+Enter`/`Ctrl+Shift+G`.
 - Added experimental strict JSON-schema constrained sampling for the default `read`, `bash`, `edit`, and `write` tools under `PI_EXPERIMENTAL=1`.
 - Added a fullscreen exit output setting to choose between printing the final transcript and only a session resume hint.
-- Added the `defaultTools` setting for configuring the initial tool allowlist globally or per project.
+- Added the `defaultTools` setting for configuring the initial built-in tool selection globally or per project.
 
 ### Changed
 

packages/coding-agent/docs/settings.md

@@ -204,9 +204,9 @@ Keep `retry.provider.maxRetries` at `0` unless provider-level retries are explic
 
 | Setting | Type | Default | Description |
 |---------|------|---------|-------------|
-| `defaultTools` | string[] | - | Initial tool allowlist. When omitted, Pi uses its standard defaults |
+| `defaultTools` | string[] | - | Built-in tools enabled initially. When omitted, Pi uses its standard defaults |
 
-`defaultTools` applies to built-in, extension, and custom tools, like the `--tools` CLI option:
+`defaultTools` selects the built-in tools enabled at startup. Extension and SDK custom tools remain enabled:
 
 ```json
 {
@@ -214,7 +214,7 @@ Keep `retry.provider.maxRetries` at `0` unless provider-level retries are explic
 }
 ```
 
-An empty array starts with no tools. `--tools`, `--no-tools`, and `--no-builtin-tools` override this setting; `--exclude-tools` filters the resulting list. A project `defaultTools` array replaces the global array.
+An empty array starts with no built-in tools while preserving extension and SDK custom tools. `--tools` replaces this behavior with a strict allowlist for all tools, `--no-tools` disables all tools, and `--no-builtin-tools` disables the built-in defaults. `--exclude-tools` filters the resulting list. A project `defaultTools` array replaces the global array.
 
 ### Sessions
 

packages/coding-agent/src/core/sdk.ts

@@ -62,10 +62,11 @@ export interface CreateAgentSessionOptions {
 	/**
 	 * Optional allowlist of tool names.
 	 *
-	 * When omitted, pi uses the `defaultTools` setting when configured. Otherwise it
-	 * enables the default built-in tools (read, bash, edit, write) and leaves
-	 * extension/custom tools enabled unless `noTools` changes that default. When
-	 * provided, only the listed tool names are enabled.
+	 * When omitted, pi uses the `defaultTools` setting for the initial built-in
+	 * selection when configured. Otherwise it enables the default built-in tools
+	 * (read, bash, edit, write). Extension/custom tools remain enabled unless
+	 * `noTools` changes that default. When provided, only the listed tool names are
+	 * enabled.
 	 */
 	tools?: string[];
 	/** Optional denylist of tool names to disable. Applies after `tools` when both are provided. */
@@ -245,9 +246,7 @@ export async function createAgentSession(options: CreateAgentSessionOptions = {}
 
 	const defaultActiveToolNames: ToolName[] = ["read", "bash", "edit", "write"];
 	const configuredDefaultToolNames = settingsManager.getDefaultTools();
-	const allowedToolNames =
-		options.tools ??
-		(options.noTools === "all" ? [] : options.noTools === undefined ? configuredDefaultToolNames : undefined);
+	const allowedToolNames = options.tools ?? (options.noTools === "all" ? [] : undefined);
 	const excludedToolNames = options.excludeTools;
 	const excludedToolNameSet = excludedToolNames ? new Set(excludedToolNames) : undefined;
 	const initialActiveToolNames = (

packages/coding-agent/src/core/settings-manager.ts

@@ -120,7 +120,7 @@ export interface Settings {
 	terminal?: TerminalSettings;
 	images?: ImageSettings;
 	enabledModels?: string[]; // Model patterns for cycling (same format as --models CLI flag)
-	defaultTools?: string[]; // Initial tool allowlist (same format as --tools CLI flag)
+	defaultTools?: string[]; // Initial built-in tool selection
 	doubleEscapeAction?: "fork" | "tree" | "none"; // Action for double-escape with empty editor (default: "tree")
 	treeFilterMode?: "default" | "no-tools" | "user-only" | "labeled-only" | "all"; // Default filter when opening /tree
 	thinkingBudgets?: ThinkingBudgetsSettings; // Custom token budgets for thinking levels

packages/coding-agent/test/default-tools-setting.test.ts

@@ -2,14 +2,15 @@ import { existsSync, mkdirSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { getModel } from "@earendil-works/pi-ai/compat";
+import { Type } from "typebox";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import { createAgentSessionFromServices, createAgentSessionServices } from "../src/core/agent-session-services.ts";
 import { DefaultResourceLoader } from "../src/core/resource-loader.ts";
-import { type CreateAgentSessionOptions, createAgentSession } from "../src/core/sdk.ts";
+import { type CreateAgentSessionOptions, createAgentSession, type InlineExtension } from "../src/core/sdk.ts";
 import { SessionManager } from "../src/core/session-manager.ts";
 import { SettingsManager } from "../src/core/settings-manager.ts";
 
-type ToolOptions = Pick<CreateAgentSessionOptions, "tools" | "excludeTools" | "noTools">;
+type ToolOptions = Pick<CreateAgentSessionOptions, "tools" | "excludeTools" | "noTools" | "customTools">;
 
 describe("defaultTools setting", () => {
 	let tempDir: string;
@@ -27,9 +28,18 @@ describe("defaultTools setting", () => {
 		}
 	});
 
-	async function createSession(defaultTools: string[], options: ToolOptions = {}) {
+	async function createSession(
+		defaultTools: string[],
+		options: ToolOptions = {},
+		extensionFactories: InlineExtension[] = [],
+	) {
 		const settingsManager = SettingsManager.inMemory({ defaultTools });
-		const resourceLoader = new DefaultResourceLoader({ cwd: tempDir, agentDir, settingsManager });
+		const resourceLoader = new DefaultResourceLoader({
+			cwd: tempDir,
+			agentDir,
+			settingsManager,
+			extensionFactories,
+		});
 		await resourceLoader.reload();
 
 		return (
@@ -45,16 +55,65 @@ describe("defaultTools setting", () => {
 		).session;
 	}
 
-	it("uses the configured list as the initial tool allowlist", async () => {
+	it("uses the configured list as the initial built-in selection", async () => {
 		const session = await createSession(["grep", "find"]);
 
-		expect(session.getAllTools().map((tool) => tool.name)).toEqual(["grep", "find"]);
+		expect(
+			session
+				.getAllTools()
+				.map((tool) => tool.name)
+				.sort(),
+		).toEqual(["bash", "edit", "find", "grep", "ls", "read", "write"]);
 		expect(session.getActiveToolNames()).toEqual(["grep", "find"]);
 		expect(session.systemPrompt).toContain("- grep:");
 		expect(session.systemPrompt).not.toContain("- read:");
 		session.dispose();
 	});
 
+	it("keeps extension and SDK custom tools enabled", async () => {
+		const session = await createSession(
+			["grep"],
+			{
+				customTools: [
+					{
+						name: "sdk_tool",
+						label: "SDK Tool",
+						description: "SDK custom tool",
+						parameters: Type.Object({}),
+						execute: async () => ({ content: [{ type: "text", text: "ok" }], details: {} }),
+					},
+				],
+			},
+			[
+				(pi) => {
+					pi.registerTool({
+						name: "static_tool",
+						label: "Static Tool",
+						description: "Statically registered extension tool",
+						parameters: Type.Object({}),
+						execute: async () => ({ content: [{ type: "text", text: "ok" }], details: {} }),
+					});
+					pi.on("session_start", () => {
+						pi.registerTool({
+							name: "dynamic_tool",
+							label: "Dynamic Tool",
+							description: "Dynamically registered extension tool",
+							parameters: Type.Object({}),
+							execute: async () => ({ content: [{ type: "text", text: "ok" }], details: {} }),
+						});
+					});
+				},
+			],
+		);
+		await session.bindExtensions({});
+
+		expect(session.getActiveToolNames().sort()).toEqual(["dynamic_tool", "grep", "sdk_tool", "static_tool"]);
+		expect(session.getAllTools().map((tool) => tool.name)).toEqual(
+			expect.arrayContaining(["read", "dynamic_tool", "sdk_tool", "static_tool"]),
+		);
+		session.dispose();
+	});
+
 	it("preserves explicit tool option precedence", async () => {
 		const allowlistedSession = await createSession(["grep"], { tools: ["read"] });
 		expect(allowlistedSession.getActiveToolNames()).toEqual(["read"]);
@@ -79,7 +138,12 @@ describe("defaultTools setting", () => {
 			model: getModel("anthropic", "claude-sonnet-4-5")!,
 		});
 
-		expect(session.getAllTools().map((tool) => tool.name)).toEqual(["ls"]);
+		expect(
+			session
+				.getAllTools()
+				.map((tool) => tool.name)
+				.sort(),
+		).toEqual(["bash", "edit", "find", "grep", "ls", "read", "write"]);
 		expect(session.getActiveToolNames()).toEqual(["ls"]);
 		session.dispose();
 	});