new open_irods_command() and run_irods_command() methods that try to run irods commands 3 times before failing; new get_file_metadata() and get_file() has an option to use that to add file metadata to a downloaded file
uses VRPipe::Steps::irods methods to run irods commands; supplies changed details to _start_over_elements_due_to_file_metadata_change; collection picking logic improved
no longer stores undef irods_local_storage_dir metadata when there are no analysis_files; adds merged metadata of parent file to each analysis file, as well as irods metadata
store correct lane hierarchy_name; store the first sample_accession_number we see in individual->acc, not the last
updated test expectations now that some upstream metadata has changed; added some extra tests