How do I clean up iTunes Mobile Applications folder that has old versions of apps?

I am using the latest iTunes 11.0.3 on my recently new iMac. Previously I had iTunes on my MacPro. The media folder was located on one of the extra (non-boot) volumes on the MacPro (MP). When I got my iMac I changed (in the Advanced section of Preferences) the location of the media folder to point to the same folder on the MP volume as I had been using. Everything seems to work fine. I can plug in my iPhone 4s and sync which goes thru a backup step.
I was then poking around in the iTunes media folder on the MP and found that the Mobile Applications (MA) folder was full of older versions of the apps on my iPhone. They dated back to 2009, 2010 and most were 2011. A few were 2012 or 2013. I would like to get rid of the old versions as they take up space. Being that old I doubt they are useful for anything anyway. But my question is how?
I have read and searched for other threads on this topic and have not found a solution. It appears that iTunes is supposed to toss old versions into the trash. I suspect it is doing that now but for some reason has lost track of these older version. The problem here is I don't know what happened.
My inclination is to take all these app .ipa files and dump them... then do an iPhone sync and have it repopulate this MA folder. But I wasn't sure iTunes would do that. So I selected one app that is currently installed on my iPhone, found several older .ipa files in the MA folder that correspond to that app and deleted all of them. I then sync'd my iPhone and watched it go thru the Backup step. When it was done I checked my MA folder but it still had NO .ipa file for that app. Why is that? To make sure the backup step didn't place it someone unexpected, I did a system wide search for that app name (the core part of the name, not including any version numbers, etc) but it found only one match. It was old (2011) located on an all-together different MA folder so did not come from this iPhone sync.
I wish someone would clearly document what goes on during an iPhone sync when the backup location is iTunes (not iCloud). Does iTunes store the current version of each app in the MA folder? I didn't see that happen in my example above.
What does it mean to remove all .ipa files from your MA folder? It would seem that it doesn't matter EXCEPT for apps no longer available in the App Store. Otherwise I could re-install them, right?
What can I delete safely without ill consequences?
How can i indentify what to remove if I should keep the latest version around?
Help would be appreciated.
To be clear:
* I use iTunes to store my Backups, not iCloud.
* I have used Consolidate after making sure that Keep iTunes Media Folder Organizaed is checked and Copy File to iTunes Media folder is checked. It did not help here.
* Given the dates of the .ipa files in my MA folder, this problem pre-dated my recent addition of my iMac.
* I believe I'm using a new local (to my iMac) iTunes library file but my media folder is on the MP as described above. When I access iTunes app on my MP it too accesses the same media folder. It is used primarily for adding music and movies to, not iPhone apps as I now sync on the iMac.

ITunes has been a disaster for me. It is filled with all sorts of things and there is no way to reorganize any of it. I'm forced to use iTunes because I have an iPhone but the experience has convinced me that it is best to avoid Apple products and I would recommend that course for others.
The operative word here is "avoid." For products like the iPhone and iPad for which Apple has a superior product there is no choice. The problem is Apple control. That means that everything is compatible with everything else which is good. It also means that everything is limited to products that serve Apple's bottom line, which is questionable.
Hopefully, now that Apple's creative genius has sadly left us, other companies will step forward to create products that will allow us to avoid the complications of Apple. I have found iTunes to be the principal complication. iTunes regularly updates itself, practically every Sunday, and then I have to restart my computer which interrupts all the tasks that I have underway.
Despite all these updates I don't use iTunes except for the iPhone and even that is problematic. The entire experience makes me glad that I don't have an Apple since it must be very difficult for Apple users to work with Apple constantly demanding updates and restarts and proprietary software and the like.
If you're not an Apple customer, but you've been listening their hype with their execs pacing a stage clad in jeans, then read this and heed. My experience with iTunes is a warning for all. Watch out. Apple is not your friend. It's a corporation bent on control, monopoly power and coerced profiteering. We may all soon need nets to save us when Apple drives us out the window.

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Message was edited by: Count Rockula

Hey TT...sorry for the long delay in following up. But you were right on the money! I ONLY download app's via my iPod because I have two iMac's... one at home and one at work. And early on, I found that unless iTunes sync set up exactly between the two computers, my sync's would be off, games removed, highest record in the world gone, etc.
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