what I do is bounce to tracks / all my little fragments of clips in each track are combined to one wave file.
this not only makes it easier to re edit but it leaves your folder much cleaner, you know what is what.
after I have bounced all my clips I then use that audio folder cleaner tool.
it works. the CWAF works better but I still haven't figured out some small details about it.
clean audio folder is easy, it takes for ever and a day to complete but it does work well.
but remember, bounce to clips is key in organizing your folders, im retentive about my project folders.
I like to be able to look in one and know what every file is.
I began a system labeling tracks a few years ago and with BTC, everything is neat and in place.
labeling drum tracks
1.kick
2.snare
3.hihat
exc. exc. exc
this way not only is everything organized by name, but its also organized by number, this way if I send my projects to per say" producer, he looks at the folder with big enjoyment. its as easy as dragging + dropping.
its also great for future versioning of the same song / different project. just drag the tracks in.
I also recommend saving your midi files this way. normally sonar saves midi files in the project file, not in the audio folder. so if your project becomes corrupt, you've lost all your midi tracks.
after I bounce to clips and label my midi tracks, I put them in a separate folder in the project.
building a good midi library of your own is another great habit all on its own.
many midi files you make yourself can be re used on other projects to shave time off.