Removed redundant Builder.setServerCapabilities duplicate method

[Adebayo120]

While trying to integrate logging with ServerCapabilities, I discovered that we have two methods and private properties on the Builder class that store ServerCapabilities. This PR removes the duplicate, so we maintain just one interface for setting ServerCapabilities

Motivation and Context

How Has This Been Tested?

Yes

Breaking Changes

No

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
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

Additional context

[CodeWithKyrian]

Please sign your commits before we can merge

[Adebayo120]

Please sign your commits before we can merge

Done @CodeWithKyrian