Quartus source control

One other thing I'm a big fan of, though slightly off topic, is going to Assignments -> Settings -> Compilation Settings and having the output files go to a sub-directory, one I usually call qout, or whatever. Quartus puts all it's output files in this directory rather than the project directory, which I think keeps things much cleaner, and makes it much more obvious what is an output file. Just a suggestion. (And Brad's comment about not using write_sdc to overwrite your .sdc, and at most write it to a dummy file and cut and paste, is something I would strongly second...)