Currently wiring files defining services instantiated by RepositoryServiceContainer and DispatchingServiceFactory are defined in WikibaseClient's config file (as, respectively, repositoryServiceWiringFiles and dispatchingServiceWiringFiles).
Having them in the configuration does not really seem a best solution. They are not configuration. They should not be replaced by the user with some other files, neither should they be editted by user like "usual" configuration files.
On the other hand, we might want to have a way, for example for extensions, of adding more wiring files (e.g. when the extension adds a service, it might want to have it work with foreign entities too).
Possible other options, mentioned by @daniel in https://gerrit.wikimedia.org/r/#/c/325969/9/docs/options.wiki, could be having a hook that would define wiring files, or using global variables, either by having a single variable for all types of wiring files, or having separate globals for each type.