Usability improvements

[mkphuthi]

• Set a default/per job format for structure files
• Delete calc_input and env_input files for workflow scripts?
• Chained should continue on the same job if two jobs use the same env_id
• Migrate to using relative paths
• Store a database at root to be updated, this can hashcheck and update sim_inputs/calc_inputs
• Resubmit certain levels of jobs
• The IDs for distributed jobs should now go in the output files not directory names and can have a prefix and suffix specified
• Add error file from slurm in corresponding