Minor Contribution: improve error handling, logger portability, and server initialization patterns

[beer-to-code]

Description

Type of Change

• feat: New feature
• fix: Bug fix
• docs: Documentation update
• refactor: Internal code change
• test: Test-only changes
• chore: Build, CI, or tooling changes

Related Issues

Changes Made

• Fix missing break in resource content switch statement (server.ts)

The case 'json' branch was missing a break, causing fall-through to the default case. This silently overwrote JSON resource responses with double-serialized content.
Replace debug console.error with logger.debug (server.ts)

• A console.error('[DEBUG] NitroStackServer.start()...') was running on every server start. Since MCP uses STDIO for JSON-RPC, any stderr output can interfere with the protocol. Replaced with this.logger.debug() to follow the project's own logging conventions.
  Use PromptNotFoundError instead of generic Error (server.ts)

• The GetPromptRequestSchema handler threw new Error('Prompt not found: ...') while tools and resources already use their dedicated error classes (ToolNotFoundError, ResourceNotFoundError). Updated to use the existing PromptNotFoundError class from errors.ts for consistency.
  Remove console.error from Zod schema conversion (tool.ts)

• The toJsonSchema() catch block used console.error, which breaks MCP's STDIO protocol. Changed to a silent fallback with an explanatory comment.
  Use os.devNull instead of hardcoded /dev/null (logger.ts)

• The fallback logger transport used filename: '/dev/null', which doesn't exist on Windows. Replaced with Node.js built-in os.devNull for cross-platform compatibility.
  Bug Fixes (@nitrostack/cli)
  Fix non-existent createTool in generated scaffold code (init.ts)

• The createProjectFromScratch fallback template imported createTool from @nitrostack/core, which doesn't exist in the public API. Updated to use new Tool({...}), which is the correct exported class.
  Fix incorrect website URL in generated README (init.ts)

• Generated project READMEs linked to nitrostack.dev instead of nitrostack.ai

Testing

• npm run lint
• npm test
• Manual testing performed (if applicable)

Screenshots / Recordings

Checklist

• I have read and followed CONTRIBUTING.md
• I have added/updated tests where appropriate
• I have updated docs where appropriate
• I have kept this PR focused and scoped
• I have used conventional commits