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Two design options to consider:
Use fusible link wire for the first 50mm of wire from the cell in place of a traditional fuse. Fusible wire isn't as good as protecting electronics as replaceable fuses, and has a reputation of being a PITA to diagnose if blown, but provides broader protection and a neater installation.
What about using a low voltage (say 2.5V 2W-5W) zener diode in series with the shunt resistor. This will protect the cell against complete discharge if the shunt transistor or controller fails on.
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