Fix SDK tools to respect cwd option

Core tools now properly use the cwd passed to createAgentSession().
Added tool factory functions for SDK users who specify custom cwd with explicit tools.

Fixes #279

packages/coding-agent/examples/sdk/12-full-control.ts

@@ -3,6 +3,10 @@
  *
  * Replace everything - no discovery, explicit configuration.
  * Still uses OAuth from ~/.pi/agent for convenience.
+ *
+ * IMPORTANT: When providing `tools` with a custom `cwd`, use the tool factory
+ * functions (createReadTool, createBashTool, etc.) to ensure tools resolve
+ * paths relative to your cwd.
  */
 
 import { Type } from "@sinclair/typebox";
@@ -13,8 +17,8 @@ import {
 	findModel,
 	SessionManager,
 	SettingsManager,
-	readTool,
-	bashTool,
+	createReadTool,
+	createBashTool,
 	type HookFactory,
 	type CustomAgentTool,
 } from "../../src/index.js";
@@ -60,8 +64,11 @@ const settingsManager = SettingsManager.inMemory({
 	retry: { enabled: true, maxRetries: 2 },
 });
 
+// When using a custom cwd with explicit tools, use the factory functions
+const cwd = process.cwd();
+
 const { session } = await createAgentSession({
-	cwd: process.cwd(),
+	cwd,
 	agentDir: "/tmp/my-agent",
 
 	model,
@@ -71,7 +78,8 @@ const { session } = await createAgentSession({
 	systemPrompt: `You are a minimal assistant.
 Available: read, bash, status. Be concise.`,
 
-	tools: [readTool, bashTool],
+	// Use factory functions with the same cwd to ensure path resolution works correctly
+	tools: [createReadTool(cwd), createBashTool(cwd)],
 	customTools: [{ tool: statusTool }],
 	hooks: [{ factory: auditHook }],
 	skills: [],