The other day I received  an error message as I was trying to transpose (I think it was) a piece.  It suggested that the file in which Sonar X3 stores copies was full.  I moved most files from C:Windows/Cakewalk/Cakewalk Projects (or some such location) to some free disc space.  I no longer see the problem.  OK ... so that fixes it; but, I wonder if there is a default setting that prevents the buildup of the number of archived versions of  a given project  ... like save only the last two versions?  There are thousands of files (especially if an automatic save feature is used). On my reasonably powerful computer, it took 20 minutes or so to move them! 

cpkoch
I wonder if there is a default setting that prevents the buildup of the number of archived versions of  a given project  ... like save only the last two versions?  There are thousands of files (especially if an automatic save feature is used). On my reasonably powerful computer, it took 20 minutes or so to move them! 

Preferences/File/Advanced is where you need to look. Enables versioning of files and lets you decide how many versions to keep. Also has the autosave settings on the same page.

Thank you TLW!

+1, here is the reference page.
 
However, the cwp files are not huge, so what I suspect is happening is that as you make changes to audio, you are getting an audio subfolder per project that grows quickly. Take a quick look at your project folder, each CWP is probably ~2MB or less; but the audio subfolder is probably significantly bigger. A couple quick things...
 
I personally do not use auto-save. I do this manually so that I can add a descriptive name to each major step performed. Without a descriptive name, having 10,000 backups does me no good, as I will never find anything anyway. If rendering anything, I have the habit of hitting Ctrl-S (quick save) prior, so that if something goes awry I can simply close (without saving) and re-open the project to where it was. From bad experiences with undo (CTRL-Z) in other programs, I will never trust that feature in any program for life (I admittedly have rarely used CTRL-Z in SONAR).
 
For "cleaning" audio folders... I keep everything on backup drives, but when a project gets to a more finalized stage, I will again save it with a descriptive name but to a new folder, using "Per Project Audio Folders" and "Copying Audio with Project." What this does is that even if I have 300 audio files but only 20 audio tracks, only the 20 tracks needed to make the project work will copy to that new folder (not all 300). For something you have completed, this is a quicker way to clean audio, such as "Song X - Final.cwp"
 
It is also advisable to name audio tracks immediately on creation to get that descriptive name included in the wav file that is created. It can be very frustrating looking at an audio folder months later and see things like "Track 1 (Bounced 11).wav"
 
Quick Edit: It just occurred to me that Melodyne edits are saved with the cwp file, so that will make them grow. I typically try to make a habit of rendering these fairly quickly rather than saving active Region FX with a cwp.

Yup!  It's the Cakewalk/Content/Audio section of the file structure that seemed to be filling up.  Unlike many, I tend to get wrapped up in doing DAW stuff and  manually saving  escapes my consciousness.  Autosave is almost a necessity and has saved me trouble more than once!  I have a fairly good system of naming files and with the "save-time" tagged to each I don't find it difficult to find them if needed. 
 
You  remind me that I need to go through and better understand the various elements of Cakewalk's file structure.  It is quite "robust" to say the least! My Content/Audio file has over 60GB  ... pretty big in my view!  I assume much of that can be trashed keeping only the final,  XXXXX.CWP version.  Right?  
 
By the way I can't help but notice your new "mettelus profile-image".  Is that your's?  What year is it?

I save after every few changes or recording (unless I know a take or chain of MIDI edits went horribly wrong and needs re-doing). Versioning gives me automatic re-naming. At various points I'll also do a "save as" and retitle the file, so e.g. 22Sept14.cwp becomes 22Sept14a.cwp, then b, c and so on. Once through tracking I'll rename again, adding "mix" to the file name. The Windows file time stamps also help me keep track of things.

After that it's mixa, b etc. again. Repeat the process once all MIDI is bounced to audio (if there's any VSTi's involved) and so on. Ending with a project suffix of "master". It may be complicated, but it does mean I know where I've got to and the project can be resurrected from previous versions if necessary.

Once I'm only dealing with audio I'll do a save-as creating not just a new project name but a new project audio folder which will only contain the final stems/takes actually being used. The contents of the original audio folder can then be rar'd up with their relevant cwp file and archived off to long-term storage. Same once I get a final mix/edit done. The idea is to keep the amount of data on the SSD I use for audio spooling sensible - and to avoid ever having to run the slow, crawling Sonar audio cleanup tool again.

I also keep four layers of autosaves, made every 10 minutes or 10 "actions". The time it takes for X3 to write a cwp file to SSD is negligible and autosave has got me out of a mess quite a few times when either I've botched something or the PC has decided to act up in some way. It's also protection against a corrupted project file because there are always multiple recent(ish) versions as backups.

Plus I back up to an HDD after finishing working with a scheduled backup to an external drive running every night as well, but that's a different subject. Am I paranoid? Maybe, but I had three highly respected Seagate Barracudas, all under a year old, fail on me in under 12 months a few years ago...

Quick question, are you using "Per Project Audio Folders"? It seems like from your post that ALL audio from all projects is in the same folder (Content/Audio)? If so, I highly recommend shifting to per project, as one massive audio folder makes things impossible to find later on. To set Per project audio folders is in Preferences->File->Audio Data "Use Per-Project Audio Folders" (at the bottom).
 
Yes, you can clean up files by saving a project to a new folder (my projects default to F:\Cakewalk Projects so very easy to find, as I use Melodyne in stand alone often). In the "Save As" dialog, be sure to check "Copy all audio with project" (and use the per-project audio as above), and create the new folder on save.
 
I run an SSD as my main drive, so have data on a magnetic HDD (which is massive). You can assign a new folder location in Preferences->File->Folder Locations (very top) if desired. Once reassigned there, you can copy all projects from the other drive into that new location.
 
As for the car, it is a 1971 mustang convertible, and may be the last one built (rolled out of the factory 9 months to the day from the day I was born). Only 6121 were made that year, and this one has the "Mach 1" body style which carried forward into 72-73. The 71s are the only ones with chrome bumpers. It is, however, not stock... 351C with a Hurst Toploader... but as with most things I treasure it is "one-of-a-kind."