Fix documentation of --output and updated output settings.

[Lilferrit]

In order to introduce some of the features/changes requested in #241 and the comments of PR #276 a branch from the output branch was created and some new command line features were introduced.

First, the --root_ckpt_name option was added to the train sub-command. This option, if set, will add a root name to the checkpoint files, e.g. if the option is set as --root_ckpt_name foobar than the checkpoint filenames will have the format foobar.epoch=2-step=150000.ckpt. Otherwise the checkpoint files will have the original default format. The checkpoint files will still be saved to the model_save_folder_path set in the config file.

Additionally a --overwrite_output boolean flag was added to all of the sub commands which produce .log and .mztab output files. If this flag isn't set then the Casanovo CLI will raise an error if one of the output files already exists, otherwise it will overwrite the output files with the new output.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.89%. Comparing base (ac2ddec) to head (84b85c3).

❗ Current head 84b85c3 differs from pull request most recent head 18c95fb

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #348      +/-   ##
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+ Coverage   89.77%   89.89%   +0.11%     
==========================================
  Files          12       12              
  Lines         929      940      +11     
==========================================
+ Hits          834      845      +11     
  Misses         95       95              

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[Lilferrit]

Duplicate of #372.