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Although quantum communication systems are being deployed on a global scale, their realistic security certification is not yet available. Here we present a security evaluation and improvement protocol for complete quantum communication systems. The protocol subdivides a system by defining seven system implementation sub-layers based on a hierarchical order of information flow; then it categorises the known system implementation imperfections by hardness of protection and practical risk. Next, an initial analysis report lists all potential loopholes in its quantum-optical part. It is followed by interactions with the system manufacturer, testing and patching most loopholes, and re-assessing their status. Our protocol has been applied on multiple commercial quantum key distribution systems to improve their security. A detailed description of our methodology is presented with the example of a subcarrier-wave system …