Uncertain: possibly from Cruft Hall, the name of the radar laboratory of Harvard's physics department during the Second World War, which contained much old and unused technical equipment; possibly a blend of crust and fluff, both of which suggest things that are obsolete and superfluous; possibly a modified form of crust.
cruft - Computer Definition
Programming code that is redundant or poorly written. It may also refer to collections of old hardware parts that are obsolete. The term's derivation is unknown, but some think it came from Harvard University's Cruft Laboratory, where discarded equipment had been seen lying around for years.