Remove repository runner

There are 3 levels of changes in this PR, accept or reject at will:

 1. the runners have been removed from  the repositories, this has no particular consequence

 2. the various `IvoryRunner` are gone for just one `IvoryRunner` and a `RepositoryConfiguration` holding all the configuration parameters for s3, hdfs, Scoobi. Those are lazily instantiated depending on the needs (to avoid the longer initialization times with ScoobiConfiguration). The `RepositoryConfiguration` object can be accessed by any `Repository` to get its configuration.

 3. the `Codec` parameter is now part of the `RepositoryConfiguration` and is not passed around anymore

In my view this is one more preparatory step towards using `DirPaths/FilePaths`. The next step is going to be the simplification of the "hole-in-the-middle" workflows.
I just pushed here what was done in the snapshot cli app. It's indeed redundant so I removed it.