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JAR Packager should let you specify a manifest on disk that it will load from permanently, rather than making you reload it manually every time the manifest changes. Also when browsing for a manifest file, it should use filesystems (not FileChooser), e.g. using the property editor for DataObject, and should start searching in the same folder as the .jarContents.
To do this: 1. Make sure the manifest property is empty (no items). 2. Add the file as an item in the JAR recipe's contents whose target is META-INF/MANIFEST.MF