Major configuration update

[gwaybio]

This pull request represents a major update and breaking change to the configuration file processing. The PR addresses 2 of 3 (and lays the groundwork for the remaining 1/3) of #10.

The PR also simultaneously begins the foray into multi-plate options as described in broadinstitute/pooled-cell-painting-profiling-recipe#50.

Specific Updates

• I propose that we move away from module specific configuration files. So much information was redundant between the two files that instead I think we should move towards function-specific configuration files. Concretely, this means an "experiment" and an "options" configuration files.
• One remaining organizational todo could be to split this even further to create an "advanced" configuration file (see #10)
• I am adding the config processing script (config_utils.py) in this repo. It didn't make sense to me to separate the config files from the configuration processing code. I will remove this script in the recipe in a future PR.
• I have also made major enhancements to the config_utils.py script.
  • We now deal with the two new configuration files
  • It is now more clear how the file, directory, and option configurations are loaded
  • Every single time the configuration file is parsed, all configuration options are visible to the script that does the parsing. This way we don't have to have weird crossover path creation happening obscurely in the config_utils that is specific to each module.

Next Steps

Once this pull request is digested and reviewed, we will need to perform several things:

1. We need to update the config documentation files. I do not think much will need to be added, just rearranged.
2. We will need to complete the multi-plate processing strategy - this PR is only half way multi-plate

[gwaybio]

the last two commits add the command argument parser utility function from the recipe to the template. The template repo will need the command args for the multi-plate processing updated weld procedure

[ErinWeisbart]

We need to update the config documentation files. I do not think much will need to be added, just rearranged.

I'm happy to deal with the documentation update.

[gwaybio]

thanks for the helpful comments @ErinWeisbart - I addressed them in the recent commits. PR ready for another look when you get a chance

[ErinWeisbart]