From The Jargon File (version 4.4.7, 29 Dec 2003):
clean
1. adj. Used of hardware or software designs, implies ‘elegance in the
small’, that is, a design or implementation that may not hold any surprises
but does things in a way that is reasonably intuitive and relatively easy
to comprehend from the outside. The antonym is ‘grungy’ or crufty.
2. v. To remove unneeded or undesired files in a effort to reduce clutter:
“I'm cleaning up my account.” “I cleaned up the garbage and now have 100
Meg free on that partition.”