Where Quartus-II keep a list of source files?

all of the source files are listed in the .qsf file

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.