Wrong kinds of MCP errors returned in some cases

[NobodysNightmare]

Describe the bug
Since the introduction of #194 the error behaviour of the MCP server has changed. Now missing tools and violations of the input schema do not cause a protocol error (JSON RPC error) anymore, but a tool execution error (i.e. successful JSON RPC response, with MCP isError flag set to true).

At least the former seems to be in violation of the MCP spec: https://modelcontextprotocol.io/specification/2025-06-18/server/tools#error-handling

Tools use two error reporting mechanisms:

1. Protocol Errors: Standard JSON-RPC errors for issues like:
   • Unknown tools
   • Invalid arguments
   • Server errors

(highlighting mine)

To Reproduce
Steps to reproduce the behavior:

1. Create an MCP server that has an empty array of tools (MCP::Server.new(tools: []))
2. Try to call a tool

Expected behavior
A JSON RPC error response (e.g. root-level element error)

References

• PR introducing change: Show exception messages for tool call errors #194
• Relevant piece of MCP spec: https://modelcontextprotocol.io/specification/2025-06-18/server/tools#error-handling