chore: fix MCP directory configs

[tamish-max]

Summary

• align mcp-server.json with the current embercore MCP entrypoint, tool list, and released version
• replace the broken smithery.yaml path with a working stdio launcher and explicit Smithery config schema
• update example MCP client configs to use the documented embercore-engine binary and current env vars

Testing

• pnpm lint
• pnpm test
• pnpm build
• node -e "const fs=require('fs'); const yaml=require('js-yaml'); const cfg=yaml.load(fs.readFileSync('smithery.yaml','utf8')); const fn=eval(cfg.startCommand.commandFunction); console.log(JSON.stringify(fn({anthropicApiKey:'test-key',anthropicBaseUrl:'https://example.com'}))); JSON.parse(fs.readFileSync('mcp-server.json','utf8'));"