Where can I find the allow to execute file as program option in the Default elementary OS loki File manager? When I try to open a file such as jar using Java runtime a window comes up as '.......(filename) is not marked as executable.

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You should set the executable bit at least for the owner. You can right-click on the file, select Properties from the menu and set Execute on the Permissions tab: set executable bit for owner

This is the equivalent of the terminal command: chmod u+x test.jar

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