TBH, with the way I've got Puppy set-up now, if the system seems to be getting a bit on the slow side, all I do is delete the 'save' and start afresh.
The 'save' holds very little these days. Virtually every app I use - with the exception of certain small system utilities - is now a 'portable' version run from outside the 'save' (and every portable contains its configuration files in-situ). I have a script set-up that links all my 'portable' apps into the system and sets-up Menu entries simultaneously.....plus a second one that auto-installs my system utilities, along with themes, desktop background wallpaper, and other odds'n'ends.
12-15 minutes later, hey presto!.....a brand-new, 'squeaky-clean' system, with Puppy champing at the bit to get 'stuck-in' and get on with something.....
It works for moi; perhaps very 'ungeek-like' of me, but I never see the point in being so dogmatic about doing stuff the official, correct & 'proper' way that you spend all your time doing nothing
but that. At the end of the day, Puppy is still just a tool that allows me to run my software & get on with doing what
I want to do; why waste time constantly 'fettling' the system almost to the exclusion of everything else?
(Which is also why I never really understand Linux geeks to whom the OS appears to be an end in itself. An OS is something that facilitates doing other stuff; by itself, frankly, it's about as much use as a chocolate teapot.....)
But that's just my perhaps 'quirky' take on things.
Mike.