[Nexus 6 Android Development] guitardedhero:
There is a very logical reason for your reported issue and is a perfect example of why I stress to my users to ALWAYS extract and examine the contents of any flashable zip before you install it. If you are too low on space to extract a large zip you can still view the contents like apps and files of the zip and extract the small scripts to view as text to see what will occur during installation.

Patch ZERO and Patch ONE are not at all the same type of zip and might benefit greatly from having different names to suggest that each one has a completely different purpose. An unaware user might also assume Patch ONE is an update to Patch ZERO for example.

Patch ZERO is a build.prop patcher using tweak.prop which contains entries to be patched to build.prop and should be placed in /sdcard. Patch ZERO allows a user to execute a script using tweak.prop without having to install a rom.

tweak.prop backs up your original build.prop to /sdcard and then patches the /system/build.prop with entries contained in /sdcard/tweak.prop. After booting up, you should have /sdcard/build.prop.bak or /sdcard/build.prop.ori (don't remember which, doesn't matter) next to tweak.prop.

When installing/updating a rom, Patch ZERO is executed during the boot before userspace which seeks tweak.prop and if found, will take the new rom's build.prop, make a backup copy to /sdcard or replace the previous one, and patch the new rom's /system/build.prop with its entries without any action needed by you as this will occur automatically if tweak.prop is on /data or /storage. /storage or /sdcard is recommended as it survives a custom recovery Factory Reset. This also allows you to modify tweak.prop at any time if you wish to add/remove or edit any entry. It is important that a blank, empty line is present under the last entry in tweak.prop so that the last entry will be included in the patch.

The /sdcard/build.prop.bak is not actually used for anything other than being a way for you to manually restore the current rom's build.prop in its stock state which will require you to set 0644 permissions if any entry in the tweak.prop causes your phone to not boot, for example. This scenario would require you to do this:

Boot to recovery

Mount > System

Advanced > File Manager

Navigate to /sdcard and tap on build.prop

Select Copy

Navigate to /system, tap Paste, and Swipe to confirm

IMPORTANT!!

- You are automatically redirected to where you started in /sdcard!

Navigate to /system

Tap build.prop (the source of boot issue)

Select Delete and Swipe to confirm

Tap build.prop.bak and select Rename

Rename to build.prop and Swipe to confirm

Tap on the newly named build.prop and select chmod

Enter the value 0644 and Swipe to confirm

Reboot

That explains Patch ZERO in its entirety.

Patch ONE is a rom add-on similar to my Xperia Z5 Premium Media System add-on, though with some extra scripts but it has one glaring difference:

Patch ONE uses edited names for folders and apk's, while my add-on uses the exact names used by Sony in its Z5 Premium Marshmallow operating system. Your issue was the result of the Patch ONE installing many of the same exact apps, but with different names! I bet you're smiling now as you're beginning to fully understand what happened! You were installing a Sony Apps add-on (Patch ONE) on top of a rom with an even heavier Sony app add-on already included(ViPER|Atmos™ Xperia™ Edition rom)!

However, please know that this would have been avoided completely if Patch One had original naming schemes as Sony and this Xperia™ Edition rom does, so you can see how altering names of folders and apk's can only have a negative effect, never is it positive. Altering the names accomplishes absolutely nothing except providing an opportunity of conflicts if flashing something containing the original names.

/data installs/updates over /system apps with altered names is fine, it's only a /system install over another differently named /system install is where the issue happens. The altered names allows the install to remain as a separate installation, whereas being named the same would have simply overwritten the previous app causing no issue except maybe a downgrade if flashed over a newer apk. This is why it is important to stick with the original naming scheme.

In conclusion, on Xperia Edition rom, Patch ONE is of no use to you but Patch ZERO will work exactly as advertised by following my instructions above. If you are on another ROM than Xperia Edition rom, Patch ONE is nice if you want it to automatically install with every rom install, but I would still recommend my Xperia Media System add-on as it is a little more complete, but more importantly, the naming scheme will be identical to those used by most. Patch ZERO will still be a wonderful asset no matter what rom you decide to use. I hope that clears any confusion and sets you on the right track! :good: