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Afaik there's only one best practice right now: Do whatever works best for you.
- You may or may not want to implement Qlik Deployment Framework
- You may or may not want to use a tool like Platform Manager for Qlik Sense or Version Manager for Qlik Sense
- You may or may not want to create your own system using something like GitHub - mindspank/serializeapp in combination with Git or Apache Subversion.
Perhaps this discussion can give you additional ideas: Qlik Sense integration with Version Control Systems