Prepare Matrix for migration and improve service health checks

- Updated .gitignore to selectively track Matrix config files
  - Allow: homeserver.yaml, *.log.config
  - Exclude: *.db*, media_store/, signing keys
- Added Matrix configuration files to repository
- Fixed BookStack environment variables (APP_KEY, DB_* pattern)
- Improved health checks for BookStack, JupyterHub, and Synapse
- All services now have proper health monitoring

.gitignore

@@ -46,8 +46,13 @@ env/
 .continue/
 
 # Docker data volumes (NEVER commit these - contain private data!)
-matrix/data/
+# Matrix - allow config files but exclude sensitive data
+matrix/data/*.db*
+matrix/data/media_store/
+matrix/data/.DS_Store
 matrix/*.signing.key
+# Matrix config files (homeserver.yaml, *.log.config) are NOT ignored and will be tracked
+
 ollama/
 open-webui/
 data/uploads/
@@ -75,7 +80,8 @@ backups/
 # Logs
 *.log
 logs/
-*.log.*
+# Matrix log config is NOT a log file, allow it
+!matrix/data/*.log.config
 
 # OS specific
 .DS_Store