fix(tree): check for all synonyms of conflicting default args

[corneliusroemer]

• fix(tree): check for all synonyms of conflicting args
• chore(tests): more robust test by adding -redo to iqtree args

Description of proposed changes

See commit messages for details.

Related issue(s)

Inspired by iqtree/iqtree2#273

Checklist

• Automated checks pass
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 72.30%. Comparing base (8731851) to head (c60a97e).
Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1547      +/-   ##
==========================================
+ Coverage   72.27%   72.30%   +0.03%     
==========================================
  Files          79       79              
  Lines        8273     8273              
  Branches     1691     1691              
==========================================
+ Hits         5979     5982       +3     
+ Misses       2009     2006       -3     
  Partials      285      285              

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[corneliusroemer]

Would be nice if someone could look at this, e.g. @huddlej @victorlin @tsibley @genehack @joverlee521 @jameshadfield

[huddlej]

Thanks, @corneliusroemer! Nice to have the check for modern synonyms and also clearer to use those throughout the docs and tests (-czb has always confused me, for example, and --polytomy is much clearer).