Remove deprecated `--legacy` flag for webhooks

Remove the deprecated `--legacy` flag from the resource generation command. The current help output shows: ```text --legacy For plugin (base.go.kubebuilder.io/v4): [DEPRECATED] If set, attempts to create resource under the API directory (legacy path). This option will be removed in future versions ``` Since the flag is already marked as deprecated and states that it will be removed in a future version, it would be good to remove it from the codebase in the next major release. We added that due a breaking change in the controller-runtime a long time ago. Note that that we should remove any usage of that from all places and tests that we have to ensure the behaviour as well. The flag was added to help out people migrate their projects, more info: https://github.com/kubernetes-sigs/kubebuilder/releases/tag/v4.3.0