I use RepositoryRestController to add addititional resource methods to Spring Data Rest Entities. When I try to add links for them to my URI space using linkTo(methodOn(Controller.class).someMethod(), Spring Data Rest generates a URL without the configured basePath.
Possibly related: #1782
Workaround: use EntityLinks.linkFor(Entity.class).slash("foo).slash("bar").withRel("my-foo"), but that is of course not refactoring-safe.