Improve rate limiting configuration and scope

[kilo-code-bot]

Summary

• Add and helper functions for safer environment variable parsing
• Move rate limiter from global middleware to route-specific middleware (only applies to /api/ routes)
• Simplify rate limit error message

Changes

• Safer parsing of , , and skip options
• Rate limiting now only applies to API routes, not to Swagger docs or other endpoints
• Cleaner error message without potentially confusing rate limit details