About .tar.gz, those are supposed to keep the permission flags when packing, see for example your application launcher still being executable after expanding a .tar.gz. So if the permissions are not set inside features, let's first check that the initial content before packing have them properly set. Another test you could make is build the .tar.gz by yourself from the content of target/products and compare whether your manual packaging keeps the executable flags.
hmm i quickly tested it once more but for me the executable flags are really not set (building this on windows)
i added the formats back to the directory-plugin
then for linux and osx tar.gz files are generated.
But looking at the "eclipse" executable then they are not set in both tar.gz files.
besides that what would be really nice if also the p2.inf install command would be followed so the jspawnhelper in the feature/jre/lib folder is also an executable:
could it be because this is created on windows?
But it should not matter where i build on the output should be the same.