Fix MCP client timeout issue: progress notifications now reset timeout by default

[Copilot]

This PR fixes the timeout issue where MCP clients would timeout after 60 seconds even when receiving progress notifications from servers performing long-running operations.

Problem

The TypeScript/JavaScript SDK was timing out after 60 seconds regardless of progress updates from the server, while the Python SDK correctly handled progress notifications by resetting the timeout. This inconsistency caused issues for users with long-running MCP tools that send periodic progress updates.

Error encountered:

McpError: MCP error -32001: Request timed out
    at Timeout.timeoutHandler (file:///.../@modelcontextprotocol/sdk/dist/esm/shared/protocol.js:282:49)
    ...
  code: -32001,
  data: { timeout: 60000 }

Root Cause

The resetTimeoutOnProgress option in RequestOptions defaulted to false, meaning that progress notifications would not reset the request timeout. This required users to explicitly opt-in to the intuitive behavior of keeping connections alive when progress is being reported.

Solution

Changed the default value of resetTimeoutOnProgress from false to true, making the TypeScript/JavaScript SDK behave consistently with the Python SDK. This ensures that:

• Progress notifications automatically reset the timeout by default
• Long-running operations with progress updates won't timeout prematurely
• Backward compatibility is maintained (users can still set resetTimeoutOnProgress: false explicitly)

Changes

• Protocol behavior: resetTimeoutOnProgress now defaults to true instead of false
• Documentation: Updated JSDoc comments to reflect the new default
• Tests: Added comprehensive test coverage for the new default behavior and updated existing tests to prevent interference

Verification

The fix has been verified with:

• All existing tests pass (670 total tests)
• New test specifically validates default timeout reset behavior
• Manual testing with demonstration script confirms progress notifications reset timeout
• Build and linting pass successfully

Example of the fix in action:

// Before: Would timeout after 60s despite progress
const result = await client.request(longRunningRequest, schema, {
  onprogress: (progress) => console.log(progress)
});

// After: Automatically resets timeout on each progress notification
const result = await client.request(longRunningRequest, schema, {
  onprogress: (progress) => console.log(progress)  // timeout resets on each call
});

Fixes #1.

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