refactor: adapt resource loader and tool wiring to pi-coding-agent 0.70

Three API shifts converge here:

- DefaultResourceLoaderOptions.agentDir is required as of 0.68 (the
  old process.cwd() fallback was removed). Pass getFusionAgentDir()
  explicitly in createFnAgent.

- createAgentSession({ tools }) is now a string[] allowlist of tool
  names, not a Tool[] array (0.68). Our boundary-wrapping via
  wrapToolsWithBoundary produces Tool instances, so we can no longer
  pass them through \`tools\`. Move them into \`customTools\` and
  suppress the built-in defaults with \`noTools: "builtin"\`. The
  wrapped tools keep the same names (read, bash, ...) as the built-ins
  they replace, so no call-site or prompt changes are needed.

- SettingsManager.create's first arg (cwd) became required (was
  optional before). Dashboard routes that previously passed
  \`undefined\` for a process-global settings view now pass
  process.cwd() to match the existing DefaultPackageManager call below.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

packages/engine/src/pi.ts

@@ -751,6 +751,7 @@ export async function createFnAgent(options: AgentOptions): Promise<AgentResult>
 
   const resourceLoader = new DefaultResourceLoader({
     cwd: options.cwd,
+    agentDir: getFusionAgentDir(),
     settingsManager,
     systemPromptOverride: () => options.systemPrompt,
     appendSystemPromptOverride: () => [],
@@ -761,13 +762,22 @@ export async function createFnAgent(options: AgentOptions): Promise<AgentResult>
   const sessionManager = options.sessionManager ?? SessionManager.inMemory();
 
   const createSessionWithModel = async (modelOverride?: typeof selectedModel) => {
+    // pi-coding-agent 0.68+: `tools` is a string[] allowlist of tool names, not
+    // Tool instances. We need boundary-wrapped versions of the built-ins, so we
+    // suppress the defaults with `noTools: "builtin"` and register our wrapped
+    // tools through `customTools` instead. The wrapped tools preserve the same
+    // names (`read`, `bash`, ...) as the built-ins they replace.
+    const customToolList: ToolDefinition[] = [
+      ...(wrappedTools as ToolDefinition[]),
+      ...(options.customTools ?? []),
+    ];
     return createAgentSession({
       cwd: options.cwd,
       authStorage,
       modelRegistry,
       resourceLoader,
-      tools: wrappedTools as any,
-      customTools: options.customTools,
+      noTools: "builtin",
+      customTools: customToolList,
       sessionManager,
       settingsManager,
       ...(modelOverride ? { model: modelOverride } : {}),