Fix all lint deprecations

[dmathieu]

level=warning msg="[config_reader] The configuration option run.skip-dirs-use-default is deprecated, please use issues.exclude-dirs-use-default."
level=warning msg="[config_reader] The configuration option output.format is deprecated, please use output.formats"
level=warning msg="[config_reader] The configuration option linters.govet.check-shadowing is deprecated. Please enable shadow instead, if you are not using enable-all."

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 60.64%. Comparing base (b4ac2be) to head (a65c697).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #581   +/-   ##
=======================================
  Coverage   60.64%   60.64%           
=======================================
  Files          40       40           
  Lines        1964     1964           
=======================================
  Hits         1191     1191           
  Misses        626      626           
  Partials      147      147           

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