Bmad File Loading

[electronsandstuff]

This PR resolves an issue loading files from Bmad using Parcel. Also some misc cleanup.

• Add output from Bmad's particle dump feature and unit test recreating the issue.
• Some cleanup of pmd_open_series
  • Refactor out find_first_iteration_file - finds first file matching filename with placeholder
  • Refactor out path_after_directory - Get the portion of the path relative to directory
  • Break out ensure_base_path_groups - Creates HDF5 groups up to iteration placeholder
• String handling methods for parsing and dealing with iterations are updated to include a padding argument: extract_iteration_from_name and replace_iteration
• The series handle is updated to include an iteration_padding parameter. In pmd_open_series, when the file being opened already exists, the padding is read from the name (file-based iterations) or group (group-based iterations) and stored. pmd_parse_iterations and pmd_open_iteration are updated to use the series padding setting.
  • All files and groups get read because iteration names like out_1000 is ambiguous and you need to confirm there are no files such as out_0001. Since Parcel supports non-contiguous groups, you can't assume the presence or lack of groups.
  • Check and error out on inconsistent padding (ie with multiple %T) and inconsistent numbering within an iteration.
  • Check for inconsistent padding across files