Fix/MCP exposure v2 TODO's (#675)

* fix: OAuth tokens secure storage for Windows & Linux

* fix(mcp): MCP Tool Re-exposure & Strict Input Validation

Fixes the MCP re-exposure bug by correctly handling tool deduplication, input validation with Ajv, and structured output (including images). Also disables experimental API betas by default to prevent 500 errors on external accounts.

* fix(mcp): skip official registry prefetch in non-first-party mode

Prevents unnecessary calls to Anthropic's MCP registry when using other API providers.

* fix(cli): disable experimental API betas by default

This prevents 500 errors from Anthropic's API when tool-calling with non-Anthropic accounts or models that don't support certain beta features.

* fix: issues raised in the PR review for #675

src/entrypoints/mcp.test.ts

@@ -0,0 +1,75 @@
+import { describe, it, expect, mock } from 'bun:test'
+import { getCombinedTools, loadReexposedMcpTools } from './mcp.js'
+import type { Tool as InternalTool } from '../Tool.js'
+import type { MCPServerConnection } from '../services/mcp/types.js'
+import type { Tool } from '@modelcontextprotocol/sdk/types.js'
+
+// Mock the MCP client service to control the tools and connections returned
+const mockGetMcpToolsCommandsAndResources = mock(async (onConnectionAttempt: any) => {})
+mock.module('../services/mcp/client.js', () => ({
+  getMcpToolsCommandsAndResources: mockGetMcpToolsCommandsAndResources
+}))
+
+describe('getCombinedTools', () => {
+  it('deduplicates builtins when mcpTools have the same name, prioritizing mcpTools', () => {
+    const builtinBash = { name: 'Bash', isMcp: false } as unknown as InternalTool
+    const builtinRead = { name: 'Read', isMcp: false } as unknown as InternalTool
+    const mcpBash = { name: 'Bash', isMcp: true } as unknown as InternalTool
+
+    const builtins = [builtinBash, builtinRead]
+    const mcpTools = [mcpBash]
+
+    const result = getCombinedTools(builtins, mcpTools)
+
+    expect(result).toHaveLength(2)
+    expect(result[0]).toBe(mcpBash)
+    expect(result[1]).toBe(builtinRead)
+  })
+})
+
+describe('loadReexposedMcpTools', () => {
+  it('loads tools and clients regardless of connection state (including needs-auth)', async () => {
+    // Setup the mock to simulate yielding a needs-auth server and a connected server
+    mockGetMcpToolsCommandsAndResources.mockImplementation(async (onConnectionAttempt) => {
+      const needsAuthClient = {
+        name: 'auth-server',
+        type: 'needs-auth',
+        config: {}
+      } as MCPServerConnection
+
+      const authTool = {
+        name: 'mcp__auth-server__authenticate',
+        isMcp: true
+      } as unknown as InternalTool
+
+      const connectedClient = {
+        name: 'connected-server',
+        type: 'connected',
+        config: {},
+        client: {}
+      } as MCPServerConnection
+
+      const connectedTool = {
+        name: 'mcp__connected-server__do_thing',
+        isMcp: true
+      } as unknown as InternalTool
+
+      // Simulate the callback behavior
+      onConnectionAttempt({ client: needsAuthClient, tools: [authTool], commands: [] })
+      onConnectionAttempt({ client: connectedClient, tools: [connectedTool], commands: [] })
+    })
+
+    const { mcpClients, mcpTools } = await loadReexposedMcpTools()
+
+    expect(mcpClients).toHaveLength(2)
+    expect(mcpClients[0].type).toBe('needs-auth')
+    expect(mcpClients[1].type).toBe('connected')
+
+    expect(mcpTools).toHaveLength(2)
+    expect(mcpTools[0].name).toBe('mcp__auth-server__authenticate')
+    expect(mcpTools[1].name).toBe('mcp__connected-server__do_thing')
+
+    // Reset mock for other tests
+    mockGetMcpToolsCommandsAndResources.mockReset()
+  })
+})