[Server] Fix: standardize error handling across handlers with MCP specificatio…

[CodeWithKyrian]

This PR standardizes error handling across all MCP handlers to comply with the MCP specification and provide better error visibility to clients while maintaining security.

Motivation & Context

• MCP Specification Compliance: Tool execution errors were incorrectly returned as JSON-RPC errors instead of CallToolResult with isError=true as required by the MCP specification
• Poor Error Visibility: Generic exception catching prevented actual error messages from reaching clients, making debugging difficult
• Unclear docs: Documentation didn't clearly specify which exceptions developers should throw in their handlers
• Inconsistent Patterns: Different handlers used different exception handling approaches

What's Changed

• CallToolHandler: ToolCallException now returns Response with CallToolResult(isError=true) instead of JSON-RPC Error
• ReadResourceHandler: ResourceReadException now forwards actual exception messages to clients
• GetPromptHandler: PromptGetException now forwards actual exception messages to clients
• Exception Handling: All handlers now catch only specific domain exceptions, with generic exceptions returning generic error messages
• Documentation: Updated with explicit guidance on which exceptions to use for each handler type
• Updated tests for both domain-specific and generic exception scenarios
• Exception-Driven Reference Provider: ReferenceProviderInterface methods now throw ToolNotFoundException, ResourceNotFoundException, and PromptNotFoundException instead of returning null, with proper exception handling in all handlers
• Simplified Exception Constructors: Not found exceptions now accept simple string parameters (name/URI) instead of request objects, making them more reusable across the codebase

Breaking Changes

Minor: ToolCallException, ResourceReadException and PromptGetException constructors now accept simple message strings instead of request objects. This aligns with documented usage patterns