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/test/agent-session-compaction.test.ts

@@ -18,7 +18,7 @@ import { AuthStorage } from "../src/core/auth-storage.js";
 import { ModelRegistry } from "../src/core/model-registry.js";
 import { SessionManager } from "../src/core/session-manager.js";
 import { SettingsManager } from "../src/core/settings-manager.js";
-import { codingTools } from "../src/core/tools/index.js";
+import { createCodingTools } from "../src/index.js";
 import { API_KEY, createTestResourceLoader } from "./utilities.js";
 
 describe.skipIf(!API_KEY)("AgentSession compaction e2e", () => {
@@ -52,7 +52,7 @@ describe.skipIf(!API_KEY)("AgentSession compaction e2e", () => {
 			initialState: {
 				model,
 				systemPrompt: "You are a helpful assistant. Be concise.",
-				tools: codingTools,
+				tools: createCodingTools(process.cwd()),
 			},
 		});
 

packages/coding-agent/test/bash-close-hang-windows.test.ts

@@ -3,8 +3,8 @@ import { existsSync, mkdirSync, readFileSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
-import { executeBash } from "../src/core/bash-executor.js";
-import { createBashTool } from "../src/core/tools/bash.js";
+import { executeBashWithOperations } from "../src/core/bash-executor.js";
+import { createBashTool, createLocalBashOperations } from "../src/core/tools/bash.js";
 
 function toBashSingleQuotedArg(value: string): string {
 	return `'${value.replace(/\\/g, "/").replace(/'/g, `'"'"'`)}'`;
@@ -87,9 +87,15 @@ describe.skipIf(process.platform !== "win32")("Windows child-process close handl
 		const controller = new AbortController();
 
 		try {
-			const result = await withTimeout(executeBash(command, { signal: controller.signal }), 3000, () => {
-				controller.abort();
-			});
+			const result = await withTimeout(
+				executeBashWithOperations(command, process.cwd(), createLocalBashOperations(), {
+					signal: controller.signal,
+				}),
+				3000,
+				() => {
+					controller.abort();
+				},
+			);
 
 			expect(result.output).toContain("child-exiting");
 			expect(result.exitCode).toBe(0);

packages/coding-agent/test/compaction-extensions.test.ts

@@ -21,7 +21,7 @@ import { ModelRegistry } from "../src/core/model-registry.js";
 import { SessionManager } from "../src/core/session-manager.js";
 import { SettingsManager } from "../src/core/settings-manager.js";
 import { createSyntheticSourceInfo } from "../src/core/source-info.js";
-import { codingTools } from "../src/core/tools/index.js";
+import { createCodingTools } from "../src/index.js";
 import { createTestResourceLoader } from "./utilities.js";
 
 const API_KEY = process.env.ANTHROPIC_OAUTH_TOKEN || process.env.ANTHROPIC_API_KEY;
@@ -92,7 +92,7 @@ describe.skipIf(!API_KEY)("Compaction extensions", () => {
 			initialState: {
 				model,
 				systemPrompt: "You are a helpful assistant. Be concise.",
-				tools: codingTools,
+				tools: createCodingTools(process.cwd()),
 			},
 		});
 

packages/coding-agent/test/footer-data-provider.test.ts

@@ -112,7 +112,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		mkdirSync(nestedDir, { recursive: true });
 		process.chdir(nestedDir);
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(nestedDir);
 		try {
 			expect(provider.getGitBranch()).toBe("main");
 			expect(vi.mocked(spawnSync)).not.toHaveBeenCalled();
@@ -125,7 +125,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		const repoDir = createPlainReftableRepo(tempDir);
 		process.chdir(repoDir);
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(repoDir);
 		try {
 			expect(provider.getGitBranch()).toBe("main");
 			expect(vi.mocked(spawnSync)).toHaveBeenCalledWith(
@@ -146,7 +146,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		const { worktreeDir } = createReftableWorktree(tempDir);
 		process.chdir(worktreeDir);
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(worktreeDir);
 		try {
 			expect(provider.getGitBranch()).toBe("main");
 		} finally {
@@ -159,7 +159,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		process.chdir(repoDir);
 		resolvedBranch = "";
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(repoDir);
 		try {
 			expect(provider.getGitBranch()).toBe("detached");
 		} finally {
@@ -171,7 +171,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		const { worktreeDir, reftableDir } = createReftableWorktree(tempDir);
 		process.chdir(worktreeDir);
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(worktreeDir);
 		try {
 			expect(provider.getGitBranch()).toBe("main");
 			vi.mocked(spawnSync).mockClear();
@@ -194,7 +194,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		const { worktreeDir, reftableDir } = createReftableWorktree(tempDir);
 		process.chdir(worktreeDir);
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(worktreeDir);
 		try {
 			expect(provider.getGitBranch()).toBe("main");
 			vi.mocked(execFile).mockClear();
@@ -215,7 +215,7 @@ describe("FooterDataProvider reftable branch detection", () => {
 		const { worktreeDir, reftableDir } = createReftableWorktree(tempDir);
 		process.chdir(worktreeDir);
 
-		const provider = new FooterDataProvider();
+		const provider = new FooterDataProvider(worktreeDir);
 		try {
 			expect(provider.getGitBranch()).toBe("main");
 			resolvedBranch = "foo";

packages/coding-agent/test/prompt-templates.test.ts

@@ -12,6 +12,7 @@ import { mkdirSync, rmSync, writeFileSync } from "fs";
 import { tmpdir } from "os";
 import { join } from "path";
 import { afterAll, describe, expect, test } from "vitest";
+import { getAgentDir } from "../src/config.js";
 import { loadPromptTemplates, parseCommandArgs, substituteArgs } from "../src/core/prompt-templates.js";
 
 // ============================================================================
@@ -406,6 +407,8 @@ You are given one or more GitHub PR URLs: $@`,
 		);
 
 		const templates = loadPromptTemplates({
+			cwd: process.cwd(),
+			agentDir: getAgentDir(),
 			promptPaths: [testDir],
 			includeDefaults: false,
 		});
@@ -427,6 +430,8 @@ Wrap it. Additional instructions: $ARGUMENTS`,
 		);
 
 		const templates = loadPromptTemplates({
+			cwd: process.cwd(),
+			agentDir: getAgentDir(),
 			promptPaths: [testDir],
 			includeDefaults: false,
 		});
@@ -447,6 +452,8 @@ Audit changelog entries for all commits since the last release.`,
 		);
 
 		const templates = loadPromptTemplates({
+			cwd: process.cwd(),
+			agentDir: getAgentDir(),
 			promptPaths: [testDir],
 			includeDefaults: false,
 		});
@@ -467,6 +474,8 @@ Do something`,
 		);
 
 		const templates = loadPromptTemplates({
+			cwd: process.cwd(),
+			agentDir: getAgentDir(),
 			promptPaths: [testDir],
 			includeDefaults: false,
 		});
@@ -487,6 +496,8 @@ Analyze GitHub issue(s): $ARGUMENTS`,
 		);
 
 		const templates = loadPromptTemplates({
+			cwd: process.cwd(),
+			agentDir: getAgentDir(),
 			promptPaths: [testDir],
 			includeDefaults: false,
 		});

packages/coding-agent/test/skills.test.ts

@@ -354,6 +354,7 @@ describe("skills", () => {
 				agentDir: emptyAgentDir,
 				cwd: emptyCwd,
 				skillPaths: [join(fixturesDir, "valid-skill")],
+				includeDefaults: true,
 			});
 			expect(skills).toHaveLength(1);
 			expect(skills[0].sourceInfo.scope).toBe("temporary");
@@ -365,6 +366,7 @@ describe("skills", () => {
 				agentDir: emptyAgentDir,
 				cwd: emptyCwd,
 				skillPaths: ["/non/existent/path"],
+				includeDefaults: true,
 			});
 			expect(skills).toHaveLength(0);
 			expect(diagnostics.some((d: ResourceDiagnostic) => d.message.includes("does not exist"))).toBe(true);
@@ -376,11 +378,13 @@ describe("skills", () => {
 				agentDir: emptyAgentDir,
 				cwd: emptyCwd,
 				skillPaths: ["~/.pi/agent/skills"],
+				includeDefaults: true,
 			});
 			const { skills: withoutTilde } = loadSkills({
 				agentDir: emptyAgentDir,
 				cwd: emptyCwd,
 				skillPaths: [homeSkillsDir],
+				includeDefaults: true,
 			});
 			expect(withTilde.length).toBe(withoutTilde.length);
 		});

packages/coding-agent/test/system-prompt.test.ts

@@ -8,6 +8,7 @@ describe("buildSystemPrompt", () => {
 				selectedTools: [],
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt).toContain("Available tools:\n(none)");
@@ -18,6 +19,7 @@ describe("buildSystemPrompt", () => {
 				selectedTools: [],
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt).toContain("Show file paths clearly");
@@ -35,6 +37,7 @@ describe("buildSystemPrompt", () => {
 				},
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt).toContain("- read:");
@@ -53,6 +56,7 @@ describe("buildSystemPrompt", () => {
 				},
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt).toContain("- dynamic_tool: Run dynamic test behavior");
@@ -63,6 +67,7 @@ describe("buildSystemPrompt", () => {
 				selectedTools: ["read", "dynamic_tool"],
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt).not.toContain("dynamic_tool");
@@ -76,6 +81,7 @@ describe("buildSystemPrompt", () => {
 				promptGuidelines: ["Use dynamic_tool for project summaries."],
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt).toContain("- Use dynamic_tool for project summaries.");
@@ -87,6 +93,7 @@ describe("buildSystemPrompt", () => {
 				promptGuidelines: ["Use dynamic_tool for summaries.", "  Use dynamic_tool for summaries.  ", "   "],
 				contextFiles: [],
 				skills: [],
+				cwd: process.cwd(),
 			});
 
 			expect(prompt.match(/- Use dynamic_tool for summaries\./g)).toHaveLength(1);

packages/coding-agent/test/tool-execution-component.test.ts

@@ -40,7 +40,15 @@ describe("ToolExecutionComponent parity", () => {
 			renderResult: () => new Text("custom result", 0, 0),
 		};
 
-		const component = new ToolExecutionComponent("custom_tool", "tool-1", {}, {}, toolDefinition, createFakeTui());
+		const component = new ToolExecutionComponent(
+			"custom_tool",
+			"tool-1",
+			{},
+			{},
+			toolDefinition,
+			createFakeTui(),
+			process.cwd(),
+		);
 		expect(stripAnsi(component.render(120).join("\n"))).toContain("custom call");
 
 		component.updateResult(
@@ -69,6 +77,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			overrideDefinition,
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [], details: { diff: "+1 after", firstChangedLine: 1 }, isError: false });
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -85,6 +94,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			undefined,
 			createFakeTui(),
+			process.cwd(),
 		);
 		const rendered = stripAnsi(component.render(120).join("\n"));
 		expect(rendered).toContain("read");
@@ -119,6 +129,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			createReadToolDefinition(process.cwd()),
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "hello" }], details: undefined, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -138,6 +149,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			overrideDefinition,
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "hello" }], details: undefined, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -158,6 +170,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			overrideDefinition,
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "hello" }], details: undefined, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -179,6 +192,7 @@ describe("ToolExecutionComponent parity", () => {
 				renderResult: () => new Text("override result", 0, 0),
 			},
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "hello" }], details: undefined, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -201,6 +215,7 @@ describe("ToolExecutionComponent parity", () => {
 				renderResult: () => new Text("wrapped override result", 0, 0),
 			},
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "hello" }], details: undefined, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -221,7 +236,15 @@ describe("ToolExecutionComponent parity", () => {
 			},
 		};
 
-		const component = new ToolExecutionComponent("custom_tool", "tool-5", {}, {}, toolDefinition, createFakeTui());
+		const component = new ToolExecutionComponent(
+			"custom_tool",
+			"tool-5",
+			{},
+			{},
+			toolDefinition,
+			createFakeTui(),
+			process.cwd(),
+		);
 		component.updateResult({ content: [{ type: "text", text: "done" }], details: {}, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
 		expect(rendered).toContain("custom call shared-token");
@@ -243,6 +266,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			toolDefinition,
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "done" }], details: {}, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -261,6 +285,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			toolDefinition,
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult({ content: [{ type: "text", text: "done" }], details: {}, isError: false }, false);
 		const rendered = stripAnsi(component.render(120).join("\n"));
@@ -276,6 +301,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			createWriteToolDefinition(process.cwd()),
 			createFakeTui(),
+			process.cwd(),
 		);
 		const rendered = stripAnsi(component.render(120).join("\n"));
 		expect(rendered).toContain("one");
@@ -291,6 +317,7 @@ describe("ToolExecutionComponent parity", () => {
 			{},
 			createReadToolDefinition(process.cwd()),
 			createFakeTui(),
+			process.cwd(),
 		);
 		component.updateResult(
 			{ content: [{ type: "text", text: "one\ntwo\n" }], details: undefined, isError: false },

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

@@ -2,16 +2,26 @@ import { existsSync, mkdirSync, readFileSync, rmSync, writeFileSync } from "fs";
 import { tmpdir } from "os";
 import { join } from "path";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
-import { executeBash } from "../src/core/bash-executor.js";
-import { bashTool, createBashTool, createLocalBashOperations } from "../src/core/tools/bash.js";
-import { editTool } from "../src/core/tools/edit.js";
-import { findTool } from "../src/core/tools/find.js";
-import { grepTool } from "../src/core/tools/grep.js";
-import { lsTool } from "../src/core/tools/ls.js";
-import { readTool } from "../src/core/tools/read.js";
-import { writeTool } from "../src/core/tools/write.js";
+import { executeBashWithOperations } from "../src/core/bash-executor.js";
+import { createBashTool, createLocalBashOperations } from "../src/core/tools/bash.js";
+import {
+	createEditTool,
+	createFindTool,
+	createGrepTool,
+	createLsTool,
+	createReadTool,
+	createWriteTool,
+} from "../src/index.js";
 import * as shellModule from "../src/utils/shell.js";
 
+const readTool = createReadTool(process.cwd());
+const writeTool = createWriteTool(process.cwd());
+const editTool = createEditTool(process.cwd());
+const bashTool = createBashTool(process.cwd());
+const grepTool = createGrepTool(process.cwd());
+const findTool = createFindTool(process.cwd());
+const lsTool = createLsTool(process.cwd());
+
 // Helper to extract text from content blocks
 function getTextOutput(result: any): string {
 	return (
@@ -438,7 +448,11 @@ describe("Coding Agent Tools", () => {
 		});
 
 		it("should preserve executeBash sanitization when using local bash operations", async () => {
-			const result = await executeBash("printf '\\033[31mred\\033[0m\\r\\n'");
+			const result = await executeBashWithOperations(
+				"printf '\\033[31mred\\033[0m\\r\\n'",
+				process.cwd(),
+				createLocalBashOperations(),
+			);
 
 			expect(result.exitCode).toBe(0);
 			expect(result.output).toBe("red\n");
@@ -468,7 +482,7 @@ describe("Coding Agent Tools", () => {
 		});
 
 		it("executeBash should persist full output when truncation happens by line count only", async () => {
-			const result = await executeBash("seq 3000");
+			const result = await executeBashWithOperations("seq 3000", process.cwd(), createLocalBashOperations());
 			const fullOutputPath = result.fullOutputPath;
 
 			expect(result.truncated).toBe(true);

packages/coding-agent/test/utilities.ts

@@ -17,7 +17,7 @@ import { ModelRegistry } from "../src/core/model-registry.js";
 import type { ResourceLoader } from "../src/core/resource-loader.js";
 import { SessionManager } from "../src/core/session-manager.js";
 import { SettingsManager } from "../src/core/settings-manager.js";
-import { codingTools } from "../src/core/tools/index.js";
+import { createCodingTools } from "../src/index.js";
 
 /**
  * API key for authenticated tests. Tests using this should be wrapped in
@@ -242,7 +242,7 @@ export function createTestSession(options: TestSessionOptions = {}): TestSession
 		initialState: {
 			model,
 			systemPrompt: options.systemPrompt ?? "You are a helpful assistant. Be extremely concise.",
-			tools: codingTools,
+			tools: createCodingTools(process.cwd()),
 		},
 	});