Для Python: pip freeze > requirements.txt, перенести .env, pip install -r requirements.txt. Для Node.js: rsync без node_modules, npm ci, PM2.
# Python
pip freeze > requirements.txt
rsync -avz /var/www/myapp/ root@new-server:/var/www/myapp/
pip install -r requirements.txt
# Node.js
rsync -avz --exclude=node_modules /var/www/nodeapp/ root@new-server:/var/www/nodeapp/
npm ci && pm2 start app.js --name myapp && pm2 startup && pm2 save