Eliminating Orphaned And Redundant lpm...

have you tryed to use the quartus function to archive and restore a project ?

menue -> Project -> Archive Project

this stores all required files into one singel file

you can double clic on that file and restore it again (in a different folder)

try to compile everything to be shure it holds all those files needed.

i use this function if i send a project to Altera MySupport for example so they get everything needed.

thats the only garbage collection i know to clean up