cleaning project of unused files

What's a dead file? Just because a file isn't used in the project does not mean I want it deleted. (As a simple case, I may have two versions of a design.)

Two things that might help:

1) After compiling, archive the project and unarchive it in a new folder. The Quartus archiver tries to take only files that were used in the compile(I believe it takes everything in the main directory, so if you don't have a file structure, that could be a problem. I recommend against that in general)

2) Speaking of not putting input files in the main directory, on all new projects I go to Assignments -> Settings -> Compilation and enable output files to be written to a directory called "qout" or "results". This puts all output reports, programming files, etc. into a sub-directory. It's amazing how much this clears the clutter.