✨ Ensure 'kubebuilder alpha generate' rescaffolds with outdated plugins

[sarthaksarthak9]

Fixes: #4433

• Fixed issue where 'kubebuilder alpha generate' failed if PROJECT contained go.kubebuilder.io/v3.
• Automatically updates outdated plugin references (v3 → v4) to support scaffolding.
• Added a warning to notify users before modifying the PROJECT file.

[k8s-ci-robot]

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[camilamacedo86]

Really great job 🥇 🎉
I added some comments, and I think we need to add a test for this case.
Otherwise, it is all amazing !!!

[sarthaksarthak9]

@camilamacedo86 I noticed that updating the plugin list in getInitArgs() automatically updates the PROJECT file, even though I don’t explicitly see a save function. How is this happening? Could you help me confirm where the file update is triggered?. Also, is there still a need for updateProjectFileForAlphaGenerate() in this case?

[k8s-ci-robot]

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[k8s-ci-robot]

[APPROVALNOTIFIER] This PR is NOT APPROVED

This pull-request has been approved by: sarthaksarthak9
Once this PR has been reviewed and has the lgtm label, please assign camilamacedo86 for approval. For more information see the Code Review Process.

The full list of commands accepted by this bot can be found here.

Needs approval from an approver in each of these files:

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[sarthaksarthak9]

I'm not very experienced at writing tests. I tried implementing the test, but ran into problems that I couldn't resolve. Could we go with test in some other pr?