Phase 1: Reorganize code with concerns, services, and docs

[lmrodriguezr]

This PR implements Phase 1 of the code reorganization plan for the SeqCode Registry. It includes the following improvements:

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📌 Changes Made

1. Code Improvements

• Updated _nomenclatural_type.json.jbuilder: Safely handles cases where the object is nil or does not respond to type_of_type, returning 'unknown' as a fallback. This aligns with the API documentation and improves robustness.

2. New Concerns (Reusable Logic)

• Paginatable: Encapsulates pagination logic to avoid repetition in controllers. Provides a paginate helper method.
• Filterable: Encapsulates filtering and sorting logic. Provides apply_filters and apply_sort helper methods.
• NameFilterable: Encapsulates Name-specific filtering and sorting logic, including status mapping and special sorting cases (e.g., citations, date).

3. New Service Objects

• Name::TypeResolver: Encapsulates the logic for resolving the nomenclatural type class for a given object. Handles edge cases where the object is nil or does not respond to type_of_type.
• Name::FuzzySearch: Encapsulates the logic for performing fuzzy searches on names using PostgreSQL's similarity functions. Supports both similarity and Levenshtein distance methods.

4. Database Optimizations

• New Migration: 20260511100000_add_indexes_to_names.rb adds indexes to frequently queried columns in the names table (e.g., name, rank, status, nomenclatural_type_type). Includes composite indexes for common query patterns.

5. Documentation Improvements

• docs/api_glossary.md: A comprehensive glossary documenting all enums (status_name, kind, rank) and special fields like nomenclatural_type. Clarifies the structure of nomenclatural_type and its possible values (Name, Genome, Strain, Other, unknown).
• docs/openapi.yaml: A complete OpenAPI 3.0 specification for the API, including all endpoints, schemas, and enums. This can be used with Swagger UI or Redoc to generate interactive API documentation.

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🎯 Goals Achieved

1. Improved Maintainability: Extracted reusable logic into concerns and service objects.
2. Better Performance: Added database indexes for frequently queried columns.
3. Enhanced Documentation: Added a glossary and OpenAPI spec to clarify API behavior and enums.
4. Robustness: Safely handled edge cases in JSON responses (e.g., nomenclatural_type).

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🔜 Next Steps

• Phase 2: Split large controllers (e.g., names_controller.rb) into smaller, focused controllers.
• Phase 2: Replace JBuilder with serializers (e.g., FastJSONAPI) for consistency.
• Phase 3: Version API routes (e.g., /v1/names) and add request specs for all endpoints.

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📚 Related Issues/PRs

• Closes the need for better documentation of nomenclatural_type and other enums.
• Improves API reliability and maintainability.

Reviewers: Please focus on the new concerns, service objects, and documentation. The changes are backward-compatible and do not break existing functionality.