fix: nosubmit runs with default cluster config

[RobertArbon]

This addresses the following issues #30 and #32 and possibly impacts #28.

there were two problems here:

1. the flag nosubmit was different between the GMX and non-GMX config parsers. This was a simple fix and addresses cli-abfe -nosubmit #32
2. when using nosubmit the cluster configuration dictionary was set to None which raised an error in the Scheduler.generate_scheduler_file method.

To fix (2) I've taken a guess at what you've intended and what is sensible and made the smallest change I could. Now the nosubmit flag has no influence on the generation of a cluster configuration.

So now nosubmit will generate cluster config files taking into account the number_of_parallel_ligand_jobs and nogpu flags.

I've also made some edits to the gitignore file for the outputs from the examples

[IAlibay]

Thanks, however could you revert all the black formatting please? it makes it impossible for us to review the code changes

[RobertArbon]

Thanks, however could you revert all the black formatting please? it makes it impossible for us to review the code changes

Done - it took a few commits but I got there.

I deleted the other PR - not sure it was appropriate in the first place but now it doesn't make sense.

[philbiggin]

merge this into the main branch. thanks @RobertArbon !