Improve CRD validation and configuration initialization logic in the controller

**Current Behavior**
MeshSync needs to improve its custom resource validation logic in the controller's reconciliation loop.

**Desired Behavior**
Implement CRD validation and configuration initialization logic in the controller.

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Start by locating MeshSync's controller reconciliation loop and the custom resource definitions it handles. Read the existing validation and configuration paths to determine where initialization belongs. Done means the reconciliation logic validates CRDs and initializes configuration consistently, including the invalid-resource behavior described by the project.

Written by the indexing model from the issue text.