Updates CoverageDoctor repair and tests.

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.

If the repair fails the CM will be rolled-back to the pre-repair file state and backup files removed.
Adds runtime options to repair.

Adds option turn the file backup on or off.
Adds option to run in sandbox mode by turning copy_over to false.
Adds option to leave temporary coverage location intact.
Suppresses default subprocess error output.

Suppresses the default subprocess error output encountered when checking the validity of a corrupt HDF5 file.
Removes ugly print statement.
Adds checkpoint for missing or incorrect h5stat.
Merge pull request #89 from oceanzus/cov_dr_enhancements

CoverageDoctor Updates