fix some CLI

[hanjinliu]

Some command simply did not work.
This PR fixes them and adds more tests.

[codecov]

Codecov Report

Attention: Patch coverage is 80.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 85.03%. Comparing base (fa716c0) to head (da10acf).
Report is 3 commits behind head on main.

Files	Patch %	Lines
cylindra/cli/run.py	75.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #110      +/-   ##
==========================================
+ Coverage   84.59%   85.03%   +0.44%     
==========================================
  Files         104      106       +2     
  Lines       14939    14952      +13     
  Branches     3171     3173       +2     
==========================================
+ Hits        12638    12715      +77     
+ Misses       1474     1401      -73     
- Partials      827      836       +9     

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