System App clean-up
Cleaning system apps is the process of integrating system app updates into the Android ROM permanently, eg into the /system partition. It has been noted that in very rare circumstances this could cause the following issues:
1) On Android 4.4 running GEL launcher, cleaning-up Google Search may prevent the next boot from completing properly. If you find yourself in this situation, you will ned to either wipe data or run the following command from a PC: "adb shell su". Once the first boot has completed no other issues has been noted. Restoring/installing a third-party launcher from recovery can also solve this issue.
2) On Android 4.4, cleaning-up Google Keyboard may cause the back button and keyboard to stop functioning until next reboot. Under rare circumstances the issue may persists after next reboot, if so uninstalling Google Keyboard and restoring it to either User or System partition fixes it. This issue has mostly been found to occur when doing clean-up with Titanium Backup.
3) During the process the affected system apps are temporarily unavailable which could results in some apps temporarily failing to work or crashing. However this issue is automatically resolved at the end of the clean-up process or after rebooting the device.
4) Before cleaning many system apps, please try to do so on a non-critical app, reboot and check if the app is still ok. Then proceed with the other apps.
No other issues have been reported at this time. NB: This issue also affects apps like Titanium Backup.