How do I set the config settings for Android in Capacitor without resetting them on build

Ionic Framework ionic-v3
1

Every time I run npx cap sync or ionic capacitor run android my config settings are reset.

e.g. in the android folder
config.xml file
build.gradle file
androidmanifest.xml

Do I set these in the capacitor.config.json file?
https://capacitor.ionicframework.com/docs/basics/configuring-your-app/

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