Added preservation of request handler params

[Kevandrew]

fix(protocol): Ensure request params reach handlers and fix progress notifications

Motivation and Context

This PR fixes two critical issues within the base Protocol class (src/shared/protocol.ts):

1. Loss of Request Parameters: The params object sent by clients in JSONRPCRequest messages was being lost before reaching handlers registered via setRequestHandler. This forced developers(me) to implement workarounds. The root cause was identified as incorrect internal schema handling within the setRequestHandler wrapper logic.
2. Broken Progress Notifications: An earlier refactoring inadvertently broke the handling of notifications/progress messages, causing onprogress callbacks provided in client.request options to fail.

This fix ensures handlers receive expected params reliably and progress updates function correctly, improving SDK usability and correctness.

How Has This Been Tested?

• Verified all existing test suites pass locally after the fix (npm test).
• Confirmed previously failing tests for progress notification handling in src/shared/protocol.test.ts now pass.
• Added a new test suite (request handler params preservation) to src/shared/protocol.test.ts specifically verifying that params objects are correctly preserved and passed to handlers registered via setRequestHandler. This test failed before the fix and passes with the fix applied.

Breaking Changes

• No breaking changes. Corrects internal behavior to match expectations.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Documentation (re: expected protocol behavior)
• My code follows the repository's style guidelines
• New and existing tests pass locally (including the new test for param preservation)
• I have added appropriate error handling (within the fix for parsing errors)
• I have added tests that prove my fix is effective or that my feature works (the new request handler params preservation test)
• I have added or updated documentation as needed

Additional context

• The fix for params loss refines internal Zod schema usage in setRequestHandler/setNotificationHandler to correctly incorporate user-defined params schemas.
• The fix for progress notifications uses a dedicated parsing path for that specific internal notification type.

---

First contribution.