docs: add missing cli flags

[pcaversaccio]

What I did

I add all missing CLI flags in the docs. Furthermore, I also add a note due to the patch in #3735. Eventually, I add the missing CLI flag metadata.

How I did it

Compare the output of vyper --help with the documentation here.

How to verify it

Run vyper --help:

Commit message

docs: add missing cli flags

Description for the changelog

docs: Add missing CLI flags.

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[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (55e18f6) 84.78% compared to head (2e5ea3b) 84.81%.
Report is 5 commits behind head on master.

❗ Current head 2e5ea3b differs from pull request most recent head f79fbe7. Consider uploading reports for the commit f79fbe7 to get more accurate results

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Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3736      +/-   ##
==========================================
+ Coverage   84.78%   84.81%   +0.03%     
==========================================
  Files          92       92              
  Lines       13139    13139              
  Branches     2929     2929              
==========================================
+ Hits        11140    11144       +4     
+ Misses       1535     1531       -4     
  Partials      464      464              

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