[CLI] Allow skipping of setup tasks during first sync run

[peterjuras]

Summary

coat sync runs all setup tasks that have not been run for a coat project. While this helps to ensure that a project is configured correctly, it can hinder the workflow of getting started with a project, where a user might want to run setup tasks like creating a repository, CI/CD pipeline or deploying the project to a service or app store at a later point.

When calling the setup function without force = true, the user should be able to skip tasks and run them later. The documentation should be updated to create awareness that it is possible that setup tasks have not been run before files are merged and synced.