Customize programs by using config files and not by changing settings in UI. It will allow you to script configuration. A simple bash script will copy files where needed and you are done.
cp ./init.vim ~/.config/nvim/init.vim
Store configuration in git (Github)
Store all configuration in Github. It allows sharing configuration between machines and allows to go back in history if something is broken.
Use scripts or provisioning tools for automation
Finally, write bash scripts or use Ansible like tools to automate the whole process. After this is done turning a new laptop into a fully usable machine will be a matter of one command.
