feat(server): isolate better-sqlite3 native binary for Electron/Node coexistence

Add rebuild-native.sh script that compiles better-sqlite3 in an isolated
temp directory for system Node.js, storing the binary at packages/server/native/.
DatabaseManager and openBetterSqliteDatabase now accept nativeBinding option.
CLI auto-detects non-Electron environment and uses the isolated binary.

.gitignore

@@ -17,6 +17,7 @@ error-log-*.txt
 
 # Project
 dist/
+packages/server/native/
 .history/
 out
 .obskey