Any long term diesel storage situation, for instance a stand-by generator, a farm storage tank... even on your boat, should have a plan for regular inspection and precautions need to be taken against contamination. Precautions that will assure your diesel will remain clean and within Lloyds standard or New Zealand ISO spec. There are many articles on the care and long term storage of diesel on the BP website. Find out more at BP
For fuel hygiene the old adage filtration filtration springs to mind. ALL tanks should have more filtration than that of the engine fuel filter. One other thing you might want to consider is installing an automatic fuel polishing system. This will turn your fuel over on a regular basis, it will polish it, and you could have UV built into it, it will kill bug by action and we can even integrate it into your building or boat management system.