This commit marks a significant architectural shift, transitioning the CLQMS backend to a fully headless REST API. All view-related components have been removed to focus solely on providing a robust, stateless API for clinical laboratory workflows.
### Architectural Changes
- **Headless API Transition:**
- Removed all view files (`app/Views/v2`), associated page controllers (`PagesController`), and routes (`Routes.php`). The application no longer serves a front-end UI.
- The root endpoint (`/`) now returns a simple "Backend Running" status message.
- **Developer Tooling & Guidance:**
- Replaced `CLAUDE.md` with `GEMINI.md` to provide updated context and instructional guidelines for Gemini agents.
- Updated `.serena/project.yml` with project configuration.
### Feature Enhancements
- **Advanced Order Management (`OrderTestModel`):**
- **Test Expansion:** The `createOrder` process now automatically expands `GROUP` (panel) tests into their individual components and recursively includes all parameter dependencies for `CALC` (calculated) tests.
- **Order Comments:** Added support for attaching comments to an order via the `ordercom` table.
- **Status Tracking:** Order status updates are now correctly recorded in the `orderstatus` table.
- **Schema Alignment:** Switched from `OrderID` to `InternalOID` as the primary key for internal operations.
- **Reference Range Refactor (`TestsController`):**
- Simplified reference range logic by consolidating `refthold` and `refvset` into the main `refnum` and `reftxt` tables.
- Standardized `RefType` handling to support `NMRC`, `TEXT`, `THOLD`, and `VSET` codes from the `reference_type` ValueSet.
### Other Changes
- **Documentation:**
- `PRD.md`, `README.md`, and `TODO.md` were updated to reflect the headless architecture, refined scope, and current project priorities.
- **Database:**
- Removed obsolete `RefTHoldID` and `RefVSetID` columns from the `patres` table migration.
- **Testing:**
- Added new feature tests for `ContactController`, `OrganizationController`, and `TestsController`.
- Remove pagination from ValueSetController::index() and ValueSetModel::getValueSets()
- Delete duplicate AGENTS.md documentation (consolidated into CLAUDE.md)
- Update .gitignore to exclude .claude folder
- Add CLAUDE.md with comprehensive agent instructions for Valueset queries
- Document new Lookups static library in README.md
- Rename all controllers from X.php to XController.php format
- Add new RefTxtModel for text-based reference ranges
- Rename group_dialog.php to grp_dialog.php and remove title_dialog.php
- Add comprehensive test suite for v2/master/TestDef module
- Update Routes.php to reflect controller renames
- Remove obsolete data files (clqms_v2.sql, lab.dbml)
- Remove deprecated docs folder with outdated documentation
- Add new plans directory with ref_range_multiple_support_plan.md
- Update test migrations, seeds, and views for improved functionality
- Consolidate page controllers into unified PagesController
- Remove deprecated V2 pages, layouts, and controllers (AuthPage, DashboardPage, V2Page)
- Add Edge resource with migration and model (EdgeResModel)
- Implement new main_layout.php for consistent page structure
- Reorganize patient views into dedicated module with dialog form
- Update routing configuration in Routes.php
- Enhance AuthFilter for improved authentication handling
- Clean up unused V2 assets (CSS, JS) and legacy images
- Update README.md with latest project information
This refactoring improves code organization, removes technical debt, and
establishes a cleaner foundation for future development.
