SERVER-15549 listDatabases command should only list existent databases

The database information is split between the storage-engine database
catalog and the database metadata, which could potentially be in-memory,
but not created on disk yet. The cases where this happens are only
applicable to the Admin database.

This change makes the listDatabases command only list databases from the
storage-engine's catalog.
SERVER-15547 removed legacy tools from source tree and build configuration. make use-new-tools option a no-op
SERVER-15502 simple targeting of explain for writes in mongos

Further command refactoring postponed