I've been creating custom packages in Composer to add configuration files, preferences, LaunchAgents, etc. to software I want to install or upgrade. But when I upload the package via Jamf Admin and install it via a Policy it doesn't overwrite any files that already exist on the JAMF client machine with the same name. This is not just files in configuration directories like /Library/Application Preferences or /private/etc, but also in /Applications. For example, if Mathematica.app is already on one of our lab computers my new Mathematica package won't overwrite the older app or any of it's config files. So I have to go in and remove all the previous app(s) and config with a run before script for every install that has a conflict.
Is this by design? Or is this a safety feature that can be turned off? I'm not sure if it's Composer or the JSS that is preventing the overwrite, but I think it's happening with PKG and DMGs I create. Any help would be much appreciated.