update MCP SDK to v1.25.1 and migrate to zod v4

[ndoschek]

What it does

• Update @modelcontextprotocol/sdk from v1.15.1 to v1.25.1
• Migrate zod from v3.23.8 to v4.2.1 to avoid type conflicts
• Update MCP tool registration API from server.tool() to server.registerTool()
• Replace zod-to-json-schema with native zod toJSONSchema() method
• Remove zod-to-json-schema dependency from ai-terminal package

Fixes GH-16615

How to test

• verify the mentioned filesystem mcp server works also with the latest version:

"ai-features.mcp.mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem@latest",
        "/some/path"
      ],
      "autostart": false
    }
}

• verify the theia mcp server works and that it still provides the test-tool. start the browser backend and test in a mcp client e.g. in VS Code:

{
	"servers": {
		"theia-mcp-server": {
			"url": "http://localhost:3000/mcp",
			"type": "http"
		}
	},
	"inputs": []
}

Follow-ups

Breaking changes

• This PR introduces breaking changes and requires careful review. If yes, the breaking changes section in the changelog has been updated.

Attribution

Review checklist

• As an author, I have thoroughly tested my changes and carefully followed the review guidelines
• User-facing text is internationalized using the nls service (for details, please see the Internationalization/Localization section in the Coding Guidelines)

Reminder for reviewers

• As a reviewer, I agree to behave in accordance with the review guidelines

[fipro78]

@ndoschek
I tested it locally and I can use the filesystem server. So it looks good to me. Now I can proceed with the implementation of the roots support.

[sdirix]

I will review at the latest next week.