Is Cyanogen fully compatible with Play services and stock android apps? I am considering the upgrade of my Android Phone to Cyanogenmod as even with root, I am having several permissions problems, OTA updates removing root, etc. 

The only reason I did not yet install it is because I don't know if it is compatible with the Play Store, and apps related. As I have alot of apps downloaded through the play store, and an AppData helium backup, I want to know if the backup will be compatible with the apps in Cyanogen.

My helium backup only has the backup of App Data, rather than the entire application source, as it is more space efficient



Samsung Galaxy S5 mini SM-G800F with stock Android 4.4.2 rooted
Luckily, Cyanogenmod is in fact compatible with play services. I am not sure about the stock apps that samsung has, as I didn't even bother trying to install them. The adb backup I made before going to CM restored properly. Google Apps are copyrighted, that's why they are not there initially. You can flash the Open GApps package as I found that to work for me best.