A perfectly working program does not need any housekeeping.

In ETL processes we have to do a lot of housekeeping to clean up the mess the processes are creating while operating. These are log files, bad files, temporary tables left behind after a process crash and so on. The system works perfectly without this functionality but will eventually drown into it's own excrements after a while.

I would not call initializing a serial port housekeeping. It is merely initializing (by definition). Clearing garbage from the cyclic buffer after baud rate change would be somewhat nearer the term but it is still something one has to do right after changing the baud rate so I would not call that either with name housekeeping.

One example of housekeeping would be a relay clean-up sequence needed for antenna tuners. The antenna tuners have knife type switches that can get oxidated if not operated every now and then. Therefore if is most desirable to give them a kick or two sometimes.

Another example of housekeeping would be starting the CPU fan in reverse direction to blow out the dust it has been collecting. Never seen this in any commercial equipment though.

The correct Java term is Garbage Collection and it is just an operation that searches for dangling memory blocks and puts them into use again.