Add deprecation notices

[gnalh]

We have a few flags that have been deprecated for a while. Let's add notices that will log in sentry.

[trunk-io]

😎 Merged successfully - details.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 35.71429% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.10%. Comparing base (99314a0) to head (e192aca).

Files with missing lines	Patch %	Lines
cli/src/upload_command.rs	50.00%	5 Missing ⚠️
cli/src/validate_command.rs	0.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #811      +/-   ##
==========================================
+ Coverage   72.86%   73.10%   +0.24%     
==========================================
  Files          72       72              
  Lines       16024    16038      +14     
==========================================
+ Hits        11676    11725      +49     
+ Misses       4348     4313      -35     

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