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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