Usability improvements

[mkphuthi]

• [ ] 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
• [x] 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
• [x] The IDs for distributed jobs should now go in the output files not directory names and can have a prefix and suffix specified
• [x] Add error file from slurm in corresponding