Create custom exception hierarchy and standardize error handling

[RonaldRonnie]

Description:
Error handling patterns vary across the codebase. Need to create a consistent exception hierarchy and standardize error responses.

Expected Behavior:

• Create custom exception classes in app/exceptions.py:
  • BioAnalyzerException (base)
  • RetrievalError
  • AnalysisError
  • ValidationError
  • ConfigurationError
  • APIError
• Standardize error response format
• Add error codes for different error types
• Update all error handling to use custom exceptions

Impact:

• Inconsistent user experience
• Harder to debug issues
• Unclear error messages

Acceptance Criteria:

• Custom exception hierarchy created
• All services use custom exceptions
• Error response format standardized
• Error codes documented
• API returns consistent error format
• Tests updated to use new exceptions

Files to Update:

• Create app/exceptions.py
• Update all service files
• Update API routers
• Update error handlers