I'm using the Mini Modular package for my Nexus 5, and I've noticed it does not backup my Gmail.
I checked out the 70-gapps.sh and all I see pertaining to my Gmail is:
Code:app/Gmail2.apk
So essentially if I flash a newer CM nightly, Gmail in /system/app gets erased. What's the point of putting my apps in the /system folder if you're just gonna kill it off?
i remember when there were no scripts and you had to flash gapps EVERY night. everything isn't perfect