Filebeat modules configuration load has some inconsistencies with other beats, and between different ways of configuring it. These differences make filebeat modules configuration to be error prone with some custom configurations, or when moving from one configuration method to other.

• It is not possible to configure the same module several times in the main file (under filebeat.modules).
  • If the same module is defined several times in filebeat.modules, only the last configuration seen is applied.
  • It is possible to configure the same modules several times with autodiscover, or using filebeat.config.modules. With filebeat.config.modules it works both when the definitions are in different files or in the same one.
• Not used filesets have to be explicitly disabled if the module is used. This happens with all configuration methods in filebeat but it doesn't happen in other beats, where only the listed datasets are enabled.

We might need to refactor filebeat modules configuration in order to address these inconsistencies.