Where Quartus-II keep a list of source files?

It can get more confusing than that though, as with IP, the .qsf often only points to a .qip file(or .qsys that points to a .qip) which then points to a bunch of other files, so those files don't directly show up in the .qsf. The .map.rpt has a list of all the files read in, so you can go there. Also, after synthesis, the Project -> Add Files allows you to expand the .qip/.qsys files to show all the files they point to. On the left side there is the Hierarchy Browser, but you can also change it to a list of all Files too, so there are a number of places to find them.