feat: switch from MySQL to SQLite for zero-dependency deployment

- Rewrite db.php to use SQLite via PDO (no external DB server needed)
- Rewrite schema.sql for SQLite (AUTOINCREMENT, CHECK constraints,
  triggers for updated_at, ON CONFLICT instead of ON DUPLICATE KEY)
- Fix config.php upsert to use ON CONFLICT syntax
- Fix index.php: tag filter via json_each, vote upsert via ON CONFLICT,
  and fix protocol create route (was returning 405 for POST /api/protocols)
- Fix yaml.php seed import: replace invalid false callbacks with fn() => null,
  fix yaml_parse pos argument (-1 -> 0)
- Update Dockerfile: drop pdo_mysql/mysqli (pdo_sqlite is built in)
- Update CloudronManifest.json: remove mysql addon, bump to v0.3.0
- Update README for SQLite deployment

README.md

@@ -17,6 +17,7 @@ Protocol Droid is a web application where communities can document, share, and r
 - **Identity**: user accounts with optional SSO support
 - **YAML import/export**: protocols are fully structured YAML — portable, git-diffable, human-readable
 - **Whitelabel**: customize site name, tagline, and theme via `config.yaml`
+- **Zero-dependency database**: SQLite — no external database server required
 
 ## Architecture
 
@@ -24,7 +25,7 @@ Protocol Droid is a web application where communities can document, share, and r
 protocol-droid/
 ├── api/                  PHP backend (REST API)
 │   ├── index.php         API router (all /api/* requests)
-│   ├── db.php            Database connection + helpers (MySQL/MariaDB)
+│   ├── db.php            Database connection + helpers (SQLite via PDO)
 │   ├── auth.php          Session-based authentication
 │   ├── config.php        Site configuration
 │   └── yaml.php          YAML import/export helpers
@@ -41,7 +42,8 @@ protocol-droid/
 │   └── fishbowl-discussion.yaml
 ├── cloudron/             Cloudron deployment files
 │   └── CloudronManifest.json
-├── schema.sql            MySQL database schema
+├── data/                 SQLite database (auto-created)
+├── schema.sql            SQLite database schema
 ├── config.yaml           Whitelabel configuration
 ├── .htaccess             Apache rewrite rules
 └── README.md             This file
@@ -49,19 +51,19 @@ protocol-droid/
 
 ## Stack
 
-- **Backend**: PHP 8.x with PDO (MySQL/MariaDB)
-- **Database**: MySQL/MariaDB (Cloudron-native)
+- **Backend**: PHP 8.x with PDO (SQLite)
+- **Database**: SQLite — file-based, no server required
 - **Frontend**: Vanilla HTML/CSS/JS — no frameworks, no build step, no external dependencies
-- **Data format**: YAML for portability, MySQL for runtime
+- **Data format**: YAML for portability, SQLite for runtime
 - **Auth**: Session-based with optional SSO
 
 ## Deployment
 
 ### On Cloudron
 
-1. Create a LAMP app in Cloudron
+1. Create a LAMP app in Cloudron (no MySQL addon needed)
 2. Upload all files to the app's web root
-3. The database schema auto-initializes on first API request
+3. The database schema auto-initializes on first API request (creates `data/protocol_droid.db`)
 4. Visit the site and register — the **first user to register becomes admin**
 5. Optionally load seed protocols: sign in as admin and `POST /api/seed` (or use the API endpoint with curl: `curl -b cookies.txt -X POST https://your-site/api/seed`)
 
@@ -70,25 +72,34 @@ protocol-droid/
 ### On any LAMP server
 
 1. Upload files to your web root (or a subdirectory like `/protocol-droid/`)
-2. Create a MySQL database and user
-3. Set environment variables (or edit `api/db.php`):
-   - `MYSQL_HOST`, `MYSQL_PORT`, `MYSQL_DATABASE`, `MYSQL_USER`, `MYSQL_PASSWORD`
-4. Visit the site and register — first user becomes admin
+2. Ensure the `data/` directory is writable by the web server
+3. Visit the site and register — first user becomes admin
+
+The SQLite database file is created automatically at `data/protocol_droid.db`. To use a custom path, set the `DATABASE_PATH` environment variable.
 
 **Subdirectory deployment:** Protocol Droid works in a subdirectory (e.g. `example.com/protocol-droid/`). The root `index.php` auto-detects the base path from the server's script name. No configuration needed — just upload the files to the subdirectory and ensure `index.php` is served as the directory index (most LAMP setups do this by default with `DirectoryIndex index.php` or `.htaccess`).
 
+### With Docker
+
+```bash
+# Build and run a single container (no separate database container needed)
+docker build -t protocol-droid .
+docker run -d --name pd-web -p 8080:80 \
+  -v pd_data:/var/www/html/data \
+  protocol-droid
+```
+
+The SQLite database lives in the `pd_data` volume. The `docker-compose.yml` included in the repo runs the same setup.
+
 ### Local development
 
 ```bash
 # Start PHP built-in server
 cd protocol-droid
 php -S localhost:8000
-
-# Or with a MySQL database:
-MYSQL_HOST=localhost MYSQL_DATABASE=protocol_droid MYSQL_USER=root MYSQL_PASSWORD=secret php -S localhost:8000
 ```
 
-The first registration creates the admin account. To load the 6 sample protocols (Round Robin Check-In, Consent Decision-Making, etc.):
+The SQLite database is created automatically at `data/protocol_droid.db`. The first registration creates the admin account. To load the 6 sample protocols (Round Robin Check-In, Consent Decision-Making, etc.):
 
 ```bash
 # After registering as admin:
@@ -112,14 +123,15 @@ curl -b cookies.txt -X DELETE http://localhost:8000/api/protocols/round-robin-ch
 | `/api` | GET | API info | none |
 | `/api/config` | GET | Site configuration | none |
 | `/api/protocols` | GET | List public protocols | none |
-| `/api/protocols/:slug` | GET | Get protocol | none |
 | `/api/protocols` | POST | Create protocol | member |
+| `/api/protocols/:slug` | GET | Get protocol | none |
 | `/api/protocols/:slug` | PUT | Update protocol | author/admin |
 | `/api/protocols/:slug` | DELETE | Delete protocol | author/admin |
 | `/api/protocols/:slug/yaml` | GET | Export as YAML | none |
+| `/api/protocols/:slug/votes` | GET | Get votes for protocol | none |
 | `/api/collections` | GET | List collections | none |
-| `/api/collections/:slug` | GET | Get collection | none |
 | `/api/collections` | POST | Create collection | member |
+| `/api/collections/:slug` | GET | Get collection | none |
 | `/api/collections/:slug` | PUT | Update collection | author/admin |
 | `/api/collections/:slug` | DELETE | Delete collection | author/admin |
 | `/api/auth/register` | POST | Register | none |