Update CLI flags documentation

[Dean-Coakley]

Proposed changes

• Update flags documentation to include missing flags, updated defaults, etc.

Checklist

Before creating a PR, run through this checklist and mark each as complete.

• I have read the CONTRIBUTING document
• I have run make install-tools and have attached any dependency changes to this pull request
• If applicable, I have added tests that prove my fix is effective or that my feature works
• If applicable, I have checked that any relevant tests pass after adding my changes
• If applicable, I have updated any relevant documentation (README.md)
• If applicable, I have tested my cross-platform changes on Ubuntu 22, Redhat 8, SUSE 15 and FreeBSD 13

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[codecov-commenter]

Codecov Report

Patch coverage has no change and project coverage change: -0.18% ⚠️

Comparison is base (556f51e) 66.44% compared to head (5b2a512) 66.26%.

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #476      +/-   ##
==========================================
- Coverage   66.44%   66.26%   -0.18%     
==========================================
  Files         118      118              
  Lines       13390    13390              
==========================================
- Hits         8897     8873      -24     
- Misses       3903     3928      +25     
+ Partials      590      589       -1     

see 2 files with indirect coverage changes

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