refactor: clean up agent configs and consolidate API documentation

.gitignore

@@ -126,6 +126,5 @@ _modules/*
 /phpunit*.xml
 /public/.htaccess
 
-.serena/
+/.serena
-.claude/
 AGENTS.md

GEMINI.md

@@ -1,115 +0,0 @@
-# CLQMS (Clinical Laboratory Quality Management System) - Gemini Context
-
-This file provides context and instructional guidelines for Gemini agents working on the CLQMS repository.
-
-## 1. Project Overview
-
-**CLQMS** is a **headless REST API backend** for a Clinical Laboratory Quality Management System. It manages the complete laboratory workflow: patient registration, ordering, specimen tracking, result entry/verification, and instrument integration.
-
-*   **Type:** API-only Backend (No View Layer).
-*   **Framework:** CodeIgniter 4 (PHP 8.1+).
-*   **Database:** MySQL.
-*   **Authentication:** JWT (Stateless).
-*   **Architecture:** Modular MVC with a file-based Lookup Library.
-
-## 2. Technical Stack
-
-*   **Language:** PHP 8.1+ (PSR-compliant)
-*   **Framework:** CodeIgniter 4
-*   **Dependencies:** `firebase/php-jwt` (Auth), `phpunit/phpunit` (Testing)
-*   **Database:** MySQL (Managed via Migrations)
-*   **Entry Point:** `public/index.php` (Web), `spark` (CLI)
-
-## 3. Development Workflow & Conventions
-
-### Tool Usage Guidelines
-**Critical:** Prioritize semantic code analysis tools over generic file reading to minimize context window usage and improve accuracy.
-
-*   **Explore Code:** Use `find_symbol` or `get_symbols_overview`.
-*   **Modify Code:** Use `replace_symbol_body` for functions/classes. Use `replace_content` (regex) for small tweaks.
-*   **Add Code:** Use `insert_before_symbol` / `insert_after_symbol`.
-*   **Search:** Use `search_for_pattern`.
-*   **File Discovery:** Use `list_dir` / `find_file`.
-
-### Common Commands
-
-**Testing:**
-```bash
-# Run all tests
-vendor/bin/phpunit
-
-# Run specific test file
-vendor/bin/phpunit tests/feature/UniformShowTest.php
-
-# Run tests in a directory
-vendor/bin/phpunit app/Models
-```
-
-**Database & Migrations:**
-```bash
-# Run migrations
-spark migrate
-
-# Rollback migrations
-spark migrate:rollback
-
-# Seed database
-spark db:seed DBSeeder
-
-# Refresh all (Reset DB)
-spark migrate:refresh --seed
-```
-
-**Code Generation:**
-```bash
-spark make:model ModelName
-spark make:controller ControllerName
-spark make:migration MigrationName
-```
-
-## 4. Key Architectural Patterns
-
-### MVC Structure
-*   **Controllers (`app/Controllers/`)**: Organized by domain (Patient, Order, Test, etc.). All extend `BaseController`.
-*   **Models (`app/Models/`)**: Domain-specific data access. All extend `BaseModel`.
-    *   **UTC Handling:** Models automatically normalize dates to UTC on save and format to UTC ISO on retrieve.
-
-### Lookup System (`App\Libraries\ValueSet`)
-*   **Mechanism:** JSON file-based static data storage. **Do not use database queries for static lookups.**
-*   **Location:** `app/Libraries/Data/valuesets/*.json`.
-*   **Usage:**
-    ```php
-    use App\Libraries\ValueSet;
-    $options = ValueSet::get('gender'); // Returns dropdown options
-    $label = ValueSet::getLabel('gender', '1'); // Returns 'Female'
-    ```
-*   **Cache:** System caches these files. Run `ValueSet::clearCache()` if files are modified manually (rare).
-
-### Edge API (Instrument Integration)
-*   **Purpose:** Middleware for laboratory analyzers.
-*   **Flow:** Instrument -> `tiny-edge` -> `POST /api/edge/results` -> `edgeres` table -> Processing -> `patresult` table.
-*   **Controllers:** `EdgeController`.
-
-### Database Schema
-*   **Migrations:** Sequentially numbered (e.g., `2026-01-01-000001`).
-*   **Master Data:** `valueset`, `testdef*` (test definitions), `ref*` (reference ranges).
-*   **Transactions:** `patient`, `porder` (orders), `specimen`, `patresult`.
-
-## 5. Documentation Map
-
-*   **`README.md`**: High-level API overview and endpoint list.
-*   **`PRD.md`**: Detailed Product Requirements Document. **Read this for business logic queries.**
-*   **`CLAUDE.md`**: Original developer guide (source of these conventions).
-*   **`TODO.md`**: Current project status and roadmap.
-*   **`app/Config/Routes.php`**: API Route definitions.
-
-## 6. Testing Strategy
-
-*   **Framework:** PHPUnit 10.5+.
-*   **Location:** `tests/`.
-*   **Coverage:** Aim for high coverage on core logic (Models, Libraries).
-*   **Configuration:** `phpunit.xml.dist`.
-
-## 7. Configuration
-*   **Environment:** managed via `.env` (template in `env`).
-*   **Database Config:** `app/Config/Database.php` (uses `.env` variables).

public/api-docs.yaml

@@ -1274,12 +1274,14 @@ paths:
           application/json:
             schema:
               type: object
+              required:
+                - InternalPVID
+                - ADTCode
               properties:
-                PatientID:
+                InternalPVID:
-                  type: string
+                  type: integer
-                VisitType:
+                  description: Internal Visit ID from patvisit table
-                  type: string
+                ADTCode:
-                ADTEvent:
                   type: string
                   enum: [A01, A02, A03, A04, A08]
                   description: |
@@ -1288,6 +1290,21 @@ paths:
                     A03: Discharge
                     A04: Register
                     A08: Update
+                LocationID:
+                  type: integer
+                  description: Location/ward ID
+                AttDoc:
+                  type: string
+                  description: Attending physician
+                RefDoc:
+                  type: string
+                  description: Referring physician
+                AdmDoc:
+                  type: string
+                  description: Admitting physician
+                CnsDoc:
+                  type: string
+                  description: Consulting physician
       responses:
         '201':
           description: ADT visit created
@@ -1302,7 +1319,37 @@ paths:
         content:
           application/json:
             schema:
-              $ref: '#/components/schemas/PatientVisit'
+              type: object
+              required:
+                - PVADTID
+              properties:
+                PVADTID:
+                  type: integer
+                  description: ADT record ID
+                ADTCode:
+                  type: string
+                  enum: [A01, A02, A03, A04, A08]
+                  description: |
+                    A01: Admit
+                    A02: Transfer
+                    A03: Discharge
+                    A04: Register
+                    A08: Update
+                LocationID:
+                  type: integer
+                  description: Location/ward ID
+                AttDoc:
+                  type: string
+                  description: Attending physician
+                RefDoc:
+                  type: string
+                  description: Referring physician
+                AdmDoc:
+                  type: string
+                  description: Admitting physician
+                CnsDoc:
+                  type: string
+                  description: Consulting physician
       responses:
         '200':
           description: ADT visit updated