In the future Selenium should be used as hobbes is deprecated.https://experienceleague.adobe.com/docs/experience-manager-65/developing/components/hobbes.html?lang=en
You should configure the code structure outlined by Adobe for AEM as a Cloud pipeline. Another solution is to push code in your repo and use a build tool for packaging your code to Adobe's recommended code structure in the AEM cloud repo.
It is safe to delete any packages under/etc/packages and it will not uninstall any package.Packages under /etc/packages are just a backup for installing or uninstalling packages.The same is true for snapshots.
You can go through https://experienceleague.adobe.com/docs/experience-manager-learn/getting-started-with-aem-headless/graphql/overview.html?lang=en for Graphql.