Q: Last year I followed your directions to relocate my iTunes library to a network storage device and everything is working great, for the most part. When I download new music and videos, the files are neatly stored on the network drive as you would hope they would be. The issue is with iPhone apps: For some reason, I noticed that when new apps are downloaded off iTunes or synced from my iPhone, they are being stored in the same folder as the library database file on my computer, not with the rest of my media on the network. All I want is for the apps to be stored with the rest of my iTunes stuff on the network drive.
Is there a way to get iTunes to keep apps seperate from the library database, with the rest of my media?

– Doug
A: Prior to iTunes 9, applications were always stored in a “Mobile Applications” folder under the main library database, regardless of where you stored your media content. iTunes 9 introduces a new “iTunes Media folder” organization structure, but if you’ve upgraded from a previous version of iTunes, it will still default to using the old layout, which includes leaving the mobile applications in the main library folder. You can convert to the “iTunes Media” layout by choosing File, Library, Organize Library from the iTunes menu, and then choosing Upgrade to iTunes Media organization from the resulting dialog box.
This will reorganize your main iTunes Music folder into subfolders by media type such as Music, Podcasts, Audiobooks and Movies, replacing the older structure where your artists were listed as the top layer of folders.
This will also create an applications folder to store all of your mobile applications, and any new applications downloaded will be placed in this folder. Note, however, that your existing applications will remain in their current location in the iTunes library folder. To move these to the new folder you will need to perform another “Consolidate Library” operation similar to how you moved your iTunes media to the external hard drive in the first place. You can find more information in our article on Transferring your iTunes Library, which has been updated for iTunes 9 and the new iTunes Media organization.