refactor: Decouple MCP JSON serialization from global ContentNegotiation configuration

Problem

Caused by #664.

MCP requires specific kotlinx.serialization.json.Json settings (explicitNulls = false, encodeDefaults = true, classDiscriminatorMode = NONE), currently bundled as McpJson. The Ktor server must install ContentNegotiation with this exact configuration:

install(ContentNegotiation) {
    json(McpJson)
}

This creates two problems:

1. Easy to forget. Users who omit McpJson get silent serialization failures at runtime (e.g., explicit null fields in JSON-RPC responses). Partially addressed by auto-installation in #665.

2. Conflicts with application-wide JSON configuration. Users may need different Json settings for non-MCP routes (e.g., encodeDefaults = false, prettyPrint = true, custom naming strategies). Because Ktor's ContentNegotiation applies a single Json instance globally, there is no way to use one configuration for MCP endpoints and another for the rest of the application.

Proposal

Inline the required serialization behavior into MCP schema classes (DTOs) using kotlinx.serialization annotations, so they serialize correctly regardless of the global Json configuration.

Class-level settings override global settings, so users would be free to configure ContentNegotiation however they need:

install(ContentNegotiation) {                                                                                                                                                                                  
    json() // any configuration — MCP classes carry their own settings
}                                                                                                                                                                                                                

Start by locating McpJson, the MCP schema classes, and the ContentNegotiation setup. Check how the schema DTOs serialize under different global Json configurations, then verify that MCP-required settings remain effective without installing McpJson globally. Done means MCP endpoints retain the required JSON behavior while non-MCP routes can use their own configuration.