chore(crd): add deprecation warnings for CRD branch removed functionality

[dkarpele]

Add deprecation comments to functions, structs, constants, and flags that were removed in the CRD branch to notify users of upcoming breaking changes.

• Add deprecation notices to annotation-based functions in options.go
• Add deprecation notices to annotation-related constants in constants.go and helper.go
• Add deprecation notices to native ArgoCD client struct and methods in argocd.go
• Add deprecation notices to removed CLI flags in run.go

These deprecation warnings inform users that the CRD branch introduces a
new architecture that eliminates the need for annotation-based approaches
and native ArgoCD client configurations.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 63.64%. Comparing base (cc9f71b) to head (d4088c5).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1223      +/-   ##
==========================================
+ Coverage   63.52%   63.64%   +0.12%     
==========================================
  Files          23       23              
  Lines        3191     3202      +11     
==========================================
+ Hits         2027     2038      +11     
  Misses       1054     1054              
  Partials      110      110              

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[chengfang]

shall we say '.. will be deprecated and removed in a future release' (to emphasize removal)?

[chengfang]

for affected cli flags, can we also add a short warning message to the description field, something like: https://github.com/argoproj/argo-cd/blob/master/server/cache/cache.go#L40 ?

[chengfang]

Do you also plan to add similar deprecation message to affected docs files?

[dkarpele]

Thanks,
all comments were addressed