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You can configure which apps to synchronize using the sync.apps config setting in the fusion-config-sync section of the Helm chart. Apps can either be excluded or included. For instance, to exclude application app1 from synchronization, use the following configuration: 
cfg:
  sync:
    apps: "-app1"
To include only app1 and app2 for synchronization, use the following 
cfg:
  sync:
    apps: "app1,app2"
To include all apps for synchronization, use the following 
cfg:
  sync:
    apps: "*"