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Normally the .runtimes folder content is updated automatically when you open the UnigineEditor. The Runtimes Generator is a console tool enabling you to generate runtimes without running the Editor, right from the command line. This tool might be useful for example, when only your assets are managed by a VCS, and you'd like to trigger generation of the .runtimes folder content right after checking out the latest version from the repository and then run your application. To invoke the tool and generate your runtimes, run <UnigineSDK>/bin/RuntimesGenerator_x64 from the command prompt (no additional arguments required).
Upon successful completion of the generation process the contents of the .runtimes folder shall be updated in accordance with the assets inside the data folder.