chore: deprecate --apply and --apply-unsafe options
#2918
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Summary
This PR deprecates
--applyand--apply-unsafeoptions used inbiome checkandbiome lintcommands.The help messages are updated, and when users use those options, biome cli prints deprecation messages.
Follow up for #2898
Test Plan
I've updated the snapshot tests for
biome <lint|check> --<apply|apply-unsafe>.There are some changes in
test/cases/**. They emit some diagnostics in console and it conflicted with new deprecation diagnostics (message).So I've changed
--applyand--apply-unsafeto--writeand--write --unsafeto resolve the diagnostics conflicts.