Deprecate petablint with individual tables

[dweindl]

I think the main use case is running petablint on a full petab problem, so we don't need the option to pass individual tables. To support individual tables with the upcoming petab v2, we'd have to extend the list of files and require a version number. I don't it's worth maintaining this functionality (correct me if I am wrong), since validation of individual files is anyways rather limited.

Therefore, this adds deprecation warnings to command line arguments for individual PEtab tables and for the -y --yaml flags, which are no longer required, and the removal of which will make petablint easier to use.

Related to #271

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 0% with 20 lines in your changes missing coverage. Please review.

Project coverage is 76.09%. Comparing base (98951d1) to head (f39e1ea).

Files	Patch %	Lines
petab/petablint.py	0.00%	20 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #274      +/-   ##
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- Coverage    76.30%   76.09%   -0.22%     
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  Files           36       36              
  Lines         3224     3233       +9     
  Branches       783      786       +3     
===========================================
  Hits          2460     2460              
- Misses         559      568       +9     
  Partials       205      205              

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[dilpath]

👍

[dilpath]

I wonder if it's possible to say yaml_file_name_deprecated takes 0 arguments, i.e. it's treated as just a "flag", and instead its argument then gets treated as a positional argument, and hence saved to yaml_file_name. Anyway, not important

[dweindl]

It can be done and would slightly simplify the code, but the petablint --help output would be more confusing, I think.