Fix: Stratum1 Replication can Ignoring Missing Root Catalogs

This allows the `cvmfs_swissknife pull` command to ignore missing root catalogs when the repository is indicated to be garbage collectable. However, if anything else is not found or the repository is not garbage collectable, it still produces errors.

Furthermore this contains a (currently failing) integration test case that models an edge case where the right interplay of garbage collection and replication leads to unreachable garbage revisions in a stratum 1 backend storage. To be fixed...