Hot answers tagged data-synchronization
Essentially - you don't. iTunes is the master, the iDevice is the slave. That's the way the system is designed. It works on the assumption that you will always have plenty of room on your Mac to store data that there is no room for on the phone, so you can add it back to the phone at any time in future. I suppose it's legacy behaviour from before iCloud ...
It's a bit difficult to diagnose this with the info you've given but from experience I've found that you are able to reliably "force an sync" with any sort of iCloud data by going to System Preferences and signing out + signing back in (it'll warn you about removing iCloud data from the device, etc.) As said in the previous answer, make sure you are ...
You could use rsync like this: rsync -av --delete /Volumes/DiskA/ /Volumes/DiskB --delete option is for delete files in DiskB that was previously deleted on DiskA. If you want to schedule it to execute periodically, I suggest you to read How can I run/stop/relaunch an application automatically, at boot/login/some other time?.
rsync is certainly one way to go. The other is to use something like SuperDuper or CarbonCopyCloner which can do drive cloning/mirroring. Also, ChronoSync might be an option as well, if you need to keep track of deleted contents for any reason.
I use DropSync and have done for ages - does what you need and more and costs $8 http://www.macupdate.com/app/mac/33071/dropsync
You will need to connect the device over USB the first time before you can use iTunes Wi-Fi Sync. For installing an IPA on your iOS device, iTunes manifests can be used to install IPAs directly on the iOS device. Alternatively, the developer can distribute the app to you using TestFlight.
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