Repositories are used to store groups of related items that have been published to FME Server (similar to directories). Items such as workspaces, source data, custom formats, custom transformers, and templates can be published in to a repository.
When a custom format or custom transformer is published to a repository, workspaces in the same repository have access to those items. In other words, workspaces can link to custom formats and custom transformers that are in the same repository, whereas workspaces in a different repository cannot do so.
FME Server Security also allows control of who can download, publish, run, or remove items from a specific repository, as well as who can create new repositories.