Clearing up the design directory

Sorry, I don't have the answer for you, but I do share your pain. What I do may go a bit beyond what you're asking for. I committed only the essential files to my source control system (GIT) and frequently use the clean-up option (git-clean) which removes anything unknown to it.

Other than the design files (including the ones created with the MegaWizard), I keep only the .cdf, .qpf, .qsf, and .qdf from the main directory and delete everything else (including db/ and dse/ directories).

The .cdf is used for programming (usually trivial to reconstruct so really not that essential), .qsf is the main Quartus project file of nearly trivial contents, .qsf is the key file with all kinds of settings including pin assignments. I must admit I don't know exactly what .qdf is used for or if it's essential.

Good luck,

Tommy