gather should support simulation repeats submitted in parallel

[atravitz]

When running quickrun in parallel, the directory structure changes so that results_0, results_1, results_2 , and gather no longer works

We need to decide if gather should become more support his scenario, or if we need to be more strict about user-behavior.

[CurtisColwell]

Glad this is already here. I am running into this problem now. I changed the protocol_repeats to 1 to run each repeat separately, but it doesn't add to the currently existing .json output. Can I add the new 'protocol_result' and 'unit_results' or will this not work?

A nice solution would be adding the new repeat to the old output file instead of throwing this error:

Error: Invalid value for '-o': File 'results/easy_rbfe_mol1_solvent_mol2_solvent.json' already exists.