fix(coding-agent): remove process-cwd tool singletons and use tool-name allowlists

- switch SDK/CLI tool selection to name-based allowlists
- apply allowlists across built-in, extension, and SDK tools
- remove ambient process.cwd defaults from core tooling and resource helpers
- update tests, examples, and TUI callers for explicit cwd plumbing
- add regression coverage for extension tool filtering

closes #3452
closes #2835

packages/coding-agent/src/core/agent-session-runtime.ts

@@ -133,9 +133,6 @@ export class AgentSessionRuntime {
 	}
 
 	private apply(result: CreateAgentSessionRuntimeResult): void {
-		if (process.cwd() !== result.services.cwd) {
-			process.chdir(result.services.cwd);
-		}
 		this._session = result.session;
 		this._services = result.services;
 		this._diagnostics = result.diagnostics;
@@ -346,9 +343,6 @@ export async function createAgentSessionRuntime(
 ): Promise<AgentSessionRuntime> {
 	assertSessionCwdExists(options.sessionManager, options.cwd);
 	const result = await createRuntime(options);
-	if (process.cwd() !== result.services.cwd) {
-		process.chdir(result.services.cwd);
-	}
 	return new AgentSessionRuntime(
 		result.session,
 		result.services,

packages/coding-agent/src/core/bash-executor.ts

@@ -12,7 +12,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import stripAnsi from "strip-ansi";
 import { sanitizeBinaryOutput } from "../utils/shell.js";
-import { type BashOperations, createLocalBashOperations } from "./tools/bash.js";
+import type { BashOperations } from "./tools/bash.js";
 import { DEFAULT_MAX_BYTES, truncateTail } from "./tools/truncate.js";
 
 // ============================================================================
@@ -43,23 +43,6 @@ export interface BashResult {
 // Implementation
 // ============================================================================
 
-/**
- * Execute a bash command with optional streaming and cancellation support.
- *
- * Uses the same local BashOperations backend as createBashTool() so interactive
- * user bash and tool-invoked bash share the same process spawning behavior.
- * Sanitization, newline normalization, temp-file capture, and truncation still
- * happen in executeBashWithOperations(), so reusing the local backend does not
- * change output processing behavior.
- *
- * @param command - The bash command to execute
- * @param options - Optional streaming callback and abort signal
- * @returns Promise resolving to execution result
- */
-export function executeBash(command: string, options?: BashExecutorOptions): Promise<BashResult> {
-	return executeBashWithOperations(command, process.cwd(), createLocalBashOperations(), options);
-}
-
 /**
  * Execute a bash command using custom BashOperations.
  * Used for remote execution (SSH, containers, etc.).

packages/coding-agent/src/core/extensions/types.ts

@@ -104,7 +104,7 @@ export type TerminalInputHandler = (data: string) => { consume?: boolean; data?:
 
 /** Working indicator configuration for the interactive streaming loader. */
 export interface WorkingIndicatorOptions {
-	/** Animation frames. Use an empty array to hide the indicator entirely. */
+	/** Animation frames. Use an empty array to hide the indicator entirely. Custom frames are rendered verbatim. */
 	frames?: string[];
 	/** Frame interval in milliseconds for animated indicators. */
 	intervalMs?: number;
@@ -142,6 +142,7 @@ export interface ExtensionUIContext {
 	 * - Omit the argument to restore the default animated spinner.
 	 * - Use `frames: ["●"]` for a static indicator.
 	 * - Use `frames: []` to hide the indicator entirely.
+	 * - Custom frames are rendered as provided, so extensions must add their own colors.
 	 */
 	setWorkingIndicator(options?: WorkingIndicatorOptions): void;
 

packages/coding-agent/src/core/footer-data-provider.ts

@@ -101,7 +101,7 @@ export class FooterDataProvider {
 	private refreshPending = false;
 	private disposed = false;
 
-	constructor(cwd: string = process.cwd()) {
+	constructor(cwd: string) {
 		this.cwd = cwd;
 		this.gitPaths = findGitPaths(cwd);
 		this.setupGitWatcher();

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

@@ -25,7 +25,7 @@ export {
 	createAgentSessionFromServices,
 	createAgentSessionServices,
 } from "./agent-session-services.js";
-export { type BashExecutorOptions, type BashResult, executeBash, executeBashWithOperations } from "./bash-executor.js";
+export { type BashExecutorOptions, type BashResult, executeBashWithOperations } from "./bash-executor.js";
 export type { CompactionResult } from "./compaction/index.js";
 export { createEventBus, type EventBus, type EventBusController } from "./event-bus.js";
 // Extensions system

packages/coding-agent/src/core/prompt-templates.ts

@@ -1,7 +1,7 @@
 import { existsSync, readdirSync, readFileSync, statSync } from "fs";
 import { homedir } from "os";
 import { basename, dirname, isAbsolute, join, resolve, sep } from "path";
-import { CONFIG_DIR_NAME, getPromptsDir } from "../config.js";
+import { CONFIG_DIR_NAME } from "../config.js";
 import { parseFrontmatter } from "../utils/frontmatter.js";
 import { createSyntheticSourceInfo, type SourceInfo } from "./source-info.js";
 
@@ -175,14 +175,14 @@ function loadTemplatesFromDir(dir: string, getSourceInfo: (filePath: string) =>
 }
 
 export interface LoadPromptTemplatesOptions {
-	/** Working directory for project-local templates. Default: process.cwd() */
-	cwd?: string;
-	/** Agent config directory for global templates. Default: from getPromptsDir() */
-	agentDir?: string;
-	/** Explicit prompt template paths (files or directories) */
-	promptPaths?: string[];
-	/** Include default prompt directories. Default: true */
-	includeDefaults?: boolean;
+	/** Working directory for project-local templates. */
+	cwd: string;
+	/** Agent config directory for global templates. */
+	agentDir: string;
+	/** Explicit prompt template paths (files or directories). */
+	promptPaths: string[];
+	/** Include default prompt directories. */
+	includeDefaults: boolean;
 }
 
 function normalizePath(input: string): string {
@@ -204,11 +204,11 @@ function resolvePromptPath(p: string, cwd: string): string {
  * 2. Project: cwd/{CONFIG_DIR_NAME}/prompts/
  * 3. Explicit prompt paths
  */
-export function loadPromptTemplates(options: LoadPromptTemplatesOptions = {}): PromptTemplate[] {
-	const resolvedCwd = options.cwd ?? process.cwd();
-	const resolvedAgentDir = options.agentDir ?? getPromptsDir();
-	const promptPaths = options.promptPaths ?? [];
-	const includeDefaults = options.includeDefaults ?? true;
+export function loadPromptTemplates(options: LoadPromptTemplatesOptions): PromptTemplate[] {
+	const resolvedCwd = options.cwd;
+	const resolvedAgentDir = options.agentDir;
+	const promptPaths = options.promptPaths;
+	const includeDefaults = options.includeDefaults;
 
 	const templates: PromptTemplate[] = [];
 

packages/coding-agent/src/core/resource-loader.ts

@@ -2,7 +2,7 @@ import { existsSync, readdirSync, readFileSync, statSync } from "node:fs";
 import { homedir } from "node:os";
 import { join, resolve, sep } from "node:path";
 import chalk from "chalk";
-import { CONFIG_DIR_NAME, getAgentDir } from "../config.js";
+import { CONFIG_DIR_NAME } from "../config.js";
 import { loadThemeFromPath, type Theme } from "../modes/interactive/theme/theme.js";
 import type { ResourceDiagnostic } from "./diagnostics.js";
 
@@ -73,11 +73,12 @@ function loadContextFileFromDir(dir: string): { path: string; content: string }
 	return null;
 }
 
-export function loadProjectContextFiles(
-	options: { cwd?: string; agentDir?: string } = {},
-): Array<{ path: string; content: string }> {
-	const resolvedCwd = options.cwd ?? process.cwd();
-	const resolvedAgentDir = options.agentDir ?? getAgentDir();
+export function loadProjectContextFiles(options: {
+	cwd: string;
+	agentDir: string;
+}): Array<{ path: string; content: string }> {
+	const resolvedCwd = options.cwd;
+	const resolvedAgentDir = options.agentDir;
 
 	const contextFiles: Array<{ path: string; content: string }> = [];
 	const seenPaths = new Set<string>();
@@ -113,8 +114,8 @@ export function loadProjectContextFiles(
 }
 
 export interface DefaultResourceLoaderOptions {
-	cwd?: string;
-	agentDir?: string;
+	cwd: string;
+	agentDir: string;
 	settingsManager?: SettingsManager;
 	eventBus?: EventBus;
 	additionalExtensionPaths?: string[];
@@ -204,8 +205,8 @@ export class DefaultResourceLoader implements ResourceLoader {
 	private lastThemePaths: string[];
 
 	constructor(options: DefaultResourceLoaderOptions) {
-		this.cwd = options.cwd ?? process.cwd();
-		this.agentDir = options.agentDir ?? getAgentDir();
+		this.cwd = options.cwd;
+		this.agentDir = options.agentDir;
 		this.settingsManager = options.settingsManager ?? SettingsManager.create(this.cwd, this.agentDir);
 		this.eventBus = options.eventBus ?? createEventBus();
 		this.packageManager = new DefaultPackageManager({

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

@@ -144,7 +144,7 @@ export class FileSettingsStorage implements SettingsStorage {
 	private globalSettingsPath: string;
 	private projectSettingsPath: string;
 
-	constructor(cwd: string = process.cwd(), agentDir: string = getAgentDir()) {
+	constructor(cwd: string, agentDir: string) {
 		this.globalSettingsPath = join(agentDir, "settings.json");
 		this.projectSettingsPath = join(cwd, CONFIG_DIR_NAME, "settings.json");
 	}
@@ -256,7 +256,7 @@ export class SettingsManager {
 	}
 
 	/** Create a SettingsManager that loads from files */
-	static create(cwd: string = process.cwd(), agentDir: string = getAgentDir()): SettingsManager {
+	static create(cwd: string, agentDir: string = getAgentDir()): SettingsManager {
 		const storage = new FileSettingsStorage(cwd, agentDir);
 		return SettingsManager.fromStorage(storage);
 	}

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

@@ -374,14 +374,14 @@ function escapeXml(str: string): string {
 }
 
 export interface LoadSkillsOptions {
-	/** Working directory for project-local skills. Default: process.cwd() */
-	cwd?: string;
-	/** Agent config directory for global skills. Default: ~/.pi/agent */
-	agentDir?: string;
+	/** Working directory for project-local skills. */
+	cwd: string;
+	/** Agent config directory for global skills. */
+	agentDir: string;
 	/** Explicit skill paths (files or directories) */
-	skillPaths?: string[];
-	/** Include default skills directories. Default: true */
-	includeDefaults?: boolean;
+	skillPaths: string[];
+	/** Include default skills directories. */
+	includeDefaults: boolean;
 }
 
 function normalizePath(input: string): string {
@@ -401,8 +401,8 @@ function resolveSkillPath(p: string, cwd: string): string {
  * Load skills from all configured locations.
  * Returns skills and any validation diagnostics.
  */
-export function loadSkills(options: LoadSkillsOptions = {}): LoadSkillsResult {
-	const { cwd = process.cwd(), agentDir, skillPaths = [], includeDefaults = true } = options;
+export function loadSkills(options: LoadSkillsOptions): LoadSkillsResult {
+	const { cwd, agentDir, skillPaths, includeDefaults } = options;
 
 	// Resolve agentDir - if not provided, use default from config
 	const resolvedAgentDir = agentDir ?? getAgentDir();

packages/coding-agent/src/core/system-prompt.ts

@@ -16,8 +16,8 @@ export interface BuildSystemPromptOptions {
 	promptGuidelines?: string[];
 	/** Text to append to system prompt. */
 	appendSystemPrompt?: string;
-	/** Working directory. Default: process.cwd() */
-	cwd?: string;
+	/** Working directory. */
+	cwd: string;
 	/** Pre-loaded context files. */
 	contextFiles?: Array<{ path: string; content: string }>;
 	/** Pre-loaded skills. */
@@ -25,7 +25,7 @@ export interface BuildSystemPromptOptions {
 }
 
 /** Build the system prompt with tools, guidelines, and context */
-export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): string {
+export function buildSystemPrompt(options: BuildSystemPromptOptions): string {
 	const {
 		customPrompt,
 		selectedTools,
@@ -36,7 +36,7 @@ export function buildSystemPrompt(options: BuildSystemPromptOptions = {}): strin
 		contextFiles: providedContextFiles,
 		skills: providedSkills,
 	} = options;
-	const resolvedCwd = cwd ?? process.cwd();
+	const resolvedCwd = cwd;
 	const promptCwd = resolvedCwd.replace(/\\/g, "/");
 
 	const now = new Date();

packages/coding-agent/src/core/tools/bash.ts

@@ -444,7 +444,3 @@ export function createBashToolDefinition(
 export function createBashTool(cwd: string, options?: BashToolOptions): AgentTool<typeof bashSchema> {
 	return wrapToolDefinition(createBashToolDefinition(cwd, options));
 }
-
-/** Default bash tool using process.cwd() for backwards compatibility. */
-export const bashToolDefinition = createBashToolDefinition(process.cwd());
-export const bashTool = createBashTool(process.cwd());

packages/coding-agent/src/core/tools/edit.ts

@@ -485,7 +485,3 @@ export function createEditToolDefinition(
 export function createEditTool(cwd: string, options?: EditToolOptions): AgentTool<typeof editSchema> {
 	return wrapToolDefinition(createEditToolDefinition(cwd, options));
 }
-
-/** Default edit tool using process.cwd() for backwards compatibility. */
-export const editToolDefinition = createEditToolDefinition(process.cwd());
-export const editTool = createEditTool(process.cwd());

packages/coding-agent/src/core/tools/find.ts

@@ -368,7 +368,3 @@ export function createFindToolDefinition(
 export function createFindTool(cwd: string, options?: FindToolOptions): AgentTool<typeof findSchema> {
 	return wrapToolDefinition(createFindToolDefinition(cwd, options));
 }
-
-/** Default find tool using process.cwd() for backwards compatibility. */
-export const findToolDefinition = createFindToolDefinition(process.cwd());
-export const findTool = createFindTool(process.cwd());

packages/coding-agent/src/core/tools/grep.ts

@@ -382,7 +382,3 @@ export function createGrepToolDefinition(
 export function createGrepTool(cwd: string, options?: GrepToolOptions): AgentTool<typeof grepSchema> {
 	return wrapToolDefinition(createGrepToolDefinition(cwd, options));
 }
-
-/** Default grep tool using process.cwd() for backwards compatibility. */
-export const grepToolDefinition = createGrepToolDefinition(process.cwd());
-export const grepTool = createGrepTool(process.cwd());

packages/coding-agent/src/core/tools/ls.ts

@@ -227,7 +227,3 @@ export function createLsToolDefinition(
 export function createLsTool(cwd: string, options?: LsToolOptions): AgentTool<typeof lsSchema> {
 	return wrapToolDefinition(createLsToolDefinition(cwd, options));
 }
-
-/** Default ls tool using process.cwd() for backwards compatibility. */
-export const lsToolDefinition = createLsToolDefinition(process.cwd());
-export const lsTool = createLsTool(process.cwd());

packages/coding-agent/src/core/tools/read.ts

@@ -271,7 +271,3 @@ export function createReadToolDefinition(
 export function createReadTool(cwd: string, options?: ReadToolOptions): AgentTool<typeof readSchema> {
 	return wrapToolDefinition(createReadToolDefinition(cwd, options));
 }
-
-/** Default read tool using process.cwd() for backwards compatibility. */
-export const readToolDefinition = createReadToolDefinition(process.cwd());
-export const readTool = createReadTool(process.cwd());

packages/coding-agent/src/core/tools/write.ts

@@ -279,7 +279,3 @@ export function createWriteToolDefinition(
 export function createWriteTool(cwd: string, options?: WriteToolOptions): AgentTool<typeof writeSchema> {
 	return wrapToolDefinition(createWriteToolDefinition(cwd, options));
 }
-
-/** Default write tool using process.cwd() for backwards compatibility. */
-export const writeToolDefinition = createWriteToolDefinition(process.cwd());
-export const writeTool = createWriteTool(process.cwd());

packages/coding-agent/src/index.ts

@@ -183,8 +183,6 @@ export {
 	createReadTool,
 	createWriteTool,
 	type PromptTemplate,
-	// Pre-built tools (use process.cwd())
-	readOnlyTools,
 } from "./core/sdk.js";
 export {
 	type BranchSummaryEntry,
@@ -235,9 +233,6 @@ export {
 	type BashToolDetails,
 	type BashToolInput,
 	type BashToolOptions,
-	bashTool,
-	bashToolDefinition,
-	codingTools,
 	createBashToolDefinition,
 	createEditToolDefinition,
 	createFindToolDefinition,
@@ -252,33 +247,23 @@ export {
 	type EditToolDetails,
 	type EditToolInput,
 	type EditToolOptions,
-	editTool,
-	editToolDefinition,
 	type FindOperations,
 	type FindToolDetails,
 	type FindToolInput,
 	type FindToolOptions,
-	findTool,
-	findToolDefinition,
 	formatSize,
 	type GrepOperations,
 	type GrepToolDetails,
 	type GrepToolInput,
 	type GrepToolOptions,
-	grepTool,
-	grepToolDefinition,
 	type LsOperations,
 	type LsToolDetails,
 	type LsToolInput,
 	type LsToolOptions,
-	lsTool,
-	lsToolDefinition,
 	type ReadOperations,
 	type ReadToolDetails,
 	type ReadToolInput,
 	type ReadToolOptions,
-	readTool,
-	readToolDefinition,
 	type ToolsOptions,
 	type TruncationOptions,
 	type TruncationResult,
@@ -289,8 +274,6 @@ export {
 	type WriteToolInput,
 	type WriteToolOptions,
 	withFileMutationQueue,
-	writeTool,
-	writeToolDefinition,
 } from "./core/tools/index.js";
 // Main entry point
 export { type MainOptions, main } from "./main.js";

packages/coding-agent/src/migrations.ts

@@ -301,7 +301,7 @@ export async function showDeprecationWarnings(warnings: string[]): Promise<void>
  *
  * @returns Object with migration results and deprecation warnings
  */
-export function runMigrations(cwd: string = process.cwd()): {
+export function runMigrations(cwd: string): {
 	migratedAuthProviders: string[];
 	deprecationWarnings: string[];
 } {

packages/coding-agent/src/modes/interactive/components/tool-execution.ts

@@ -1,6 +1,6 @@
 import { Box, type Component, Container, getCapabilities, Image, Spacer, Text, type TUI } from "@mariozechner/pi-tui";
 import type { ToolDefinition, ToolRenderContext } from "../../../core/extensions/types.js";
-import { allToolDefinitions } from "../../../core/tools/index.js";
+import { createAllToolDefinitions, type ToolName } from "../../../core/tools/index.js";
 import { getTextOutput as getRenderedTextOutput } from "../../../core/tools/render-utils.js";
 import { convertToPng } from "../../../utils/image-convert.js";
 import { theme } from "../theme/theme.js";
@@ -45,14 +45,14 @@ export class ToolExecutionComponent extends Container {
 		options: ToolExecutionOptions = {},
 		toolDefinition: ToolDefinition<any, any> | undefined,
 		ui: TUI,
-		cwd: string = process.cwd(),
+		cwd: string,
 	) {
 		super();
 		this.toolName = toolName;
 		this.toolCallId = toolCallId;
 		this.args = args;
 		this.toolDefinition = toolDefinition;
-		this.builtInToolDefinition = allToolDefinitions[toolName as keyof typeof allToolDefinitions];
+		this.builtInToolDefinition = createAllToolDefinitions(cwd)[toolName as ToolName];
 		this.showImages = options.showImages ?? true;
 		this.ui = ui;
 		this.cwd = cwd;

packages/coding-agent/src/utils/shell.ts

@@ -53,7 +53,7 @@ export function getShellConfig(): { shell: string; args: string[] } {
 		return cachedShellConfig;
 	}
 
-	const settings = SettingsManager.create();
+	const settings = SettingsManager.create(process.cwd());
 	const customShellPath = settings.getShellPath();
 
 	// 1. Check user-specified shell path