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

cloudron/CloudronManifest.json

@@ -4,18 +4,14 @@
   "author": "Media Economies Design Lab, CU Boulder",
   "description": "A tool for authoring, sharing, and curating social protocols. Self-hostable and whitelabel-able.",
   "tagline": "A commons of social protocols",
-  "version": "0.1.0",
+  "version": "0.3.0",
   "healthCheckPath": "/api",
   "httpPort": 8000,
   "manifestVersion": 2,
   "website": "https://medlab.host",
   "contactEmail": "medlab@colorado.edu",
   "icon": "file://icon.png",
-  "addons": {
-    "mysql": {
-      "noDatabase": false
-    }
-  },
+  "addons": {},
   "tcpPorts": {},
   "udpPorts": {},
   "capabilities": [],