CoverageDoctor Updates

Aligns repair with analyze and CM work flow.
Modifies test for recovery based on new work flow.
Adds checks for corrupted file before calculating the size ratio.
Replaces original repair def with repair_metadata, renamed to repair
Removes log.warn statement
Adds timestamp to backup files.
Adds auto-rollback on repair failure.
Suppresses hdf5dump error messages upon inspection of invalid HDF5 file.
Adds runtme options to repair function to assist debugging and increase test coverage.