patch: deprecate old HOMEBREW_PREFIX placeholder

[cho-m]

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Uncomment deprecation for next release

[Copilot]

Pull Request Overview

This PR uncomments a deprecation warning in the EmbeddedPatch#apply method to alert users when they use the older HOMEBREW_PREFIX placeholder instead of the newer @@HOMEBREW_PREFIX@@ placeholder in patches.

Key changes:

• Enables a previously commented-out deprecation warning for the legacy HOMEBREW_PREFIX placeholder syntax in patches

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[MikeMcQuaid]

Thanks!