A repository or repo is a server that hosts program files for your distribution. Distributions host their own repositories from which you can install software with your package manager, like APT or DNF or others. If you only install software from your distribution’s repository, there’s likely no clashes with software versioning and dependencies, and the packages are about as reliable as they can be (which doesn’t mean there’s never malware). If you add third party repositories for software not available from your distributions repository, it’s more likely there will be issues, because the distribution doesn’t guarantee the packages work well together. For example, Debian and Arch don’t retrieve and install their software from the same source. They have their own servers (repositories) hosting software compiled to work with their particular distro and to be used by their chosen package manager. Flatpak (or Snap or Guix) is a separate package manager that handles it’s own dependencies and doesn’t clash with your distribution’s own software manager. Does this help?