If the keyboard layout gets lost and reverts to US on boot, configure it as you want and then import your user keyboard settings to the default system settings with sudo :

sudo defaults import com.apple.HIToolbox.plist ~/Library/Preferences/com.apple.HIToolbox.plist

Examples from https://github.com/Integralist/dotfiles/blob/cc906bd14636543e71d9c034d6507f5986a80bbd/bootstrap.sh#L7-L53

# Enable hidden files in Finder (use toggle_hidden function from ~/.bashrc)
defaults write com.apple.finder AppleShowAllFiles YES
 
# Show all file extensions in Finder
defaults write NSGlobalDomain AppleShowAllExtensions -bool true
 
# Decrease delay between repeated keys
defaults write NSGlobalDomain ApplePressAndHoldEnabled -bool false
defaults write NSGlobalDomain KeyRepeat -int 0
defaults write NSGlobalDomain InitialKeyRepeat -int 10
 
# Disable smart quotes and dashes
defaults write NSGlobalDomain NSAutomaticQuoteSubstitutionEnabled -bool false
defaults write NSGlobalDomain NSAutomaticDashSubstitutionEnabled -bool false
defaults write com.apple.TextEdit SmartQuotes -bool false
defaults write com.apple.TextEdit SmartDashes -bool false
 
# Configure menu bar clock to something useful
defaults write com.apple.menuextra.clock "DateFormat" "EEE d MMM  HH:mm:ss"
defaults write com.apple.menuextra.clock "FlashDateSeparators" 0
defaults write com.apple.menuextra.clock "IsAnalog" 0
 
# Configure Mouse Seconday Button
defaults write com.apple.mouse "enableSecondaryClick" 1
defaults write com.apple.driver.AppleBluetoothMultitouch.mouse MouseButtonMode -string "TwoButton"

Disable "You are attempting to connect to the server ..." prompt

sudo defaults write /Library/Preferences/com.apple.NetworkAuthorization AllowUnknownServers -bool YES