Fix unintended patches change in all Kustomization writes.

[etefera]

Fixes #2935 by moving the fix step out of the Write step to before the Write step (and only in the fix command).

[k8s-ci-robot]

Hi @etefera. Thanks for your PR.

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[Shell32-Natsu]

/ok-to-test

[Shell32-Natsu]

/lgtm

[Shell32-Natsu]

/cc @monopole

[k8s-ci-robot]

[APPROVALNOTIFIER] This PR is NOT APPROVED

This pull-request has been approved by: etefera
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[monopole]

/lgtm

No more passive fixes on every write. makes sense.

[monopole]

/lgtm