ITA-Solar/rh: New save input version

This version now saves nearly all the input options and files (including keyword.input, atom files, line lists, but not the input atmosphere or molecule files) to output_indata.hdf5. These can be used to improve reproducibility (exact copies of files used), and improve the re-run option. Any re-run will now use the saved input options, and a re-run can be performed even if the original input files are lost.

The documentation has been updated and contains important bug fixes.