[Android Software/Hacking General [Developers Only]] gps3dx:
Thank you for the reply !

My device is Nexus 7, running on SmoothROM v5.2.

Here is the ApG log when I create the UPDATE.zip:

ROOT= /cygdrive/d/TEMP/ApGPackages/ap
TOOL= /cygdrive/d/TEMP/ApGPackages/ap/patch_tools.tgz
ROM= /cygdrive/d/TEMP/ApGPackages/ap/SmoothROM-v5.2.zip
ROMX= D:\TEMP\APGPAC~1\ap\SMOOTH~1.ZIP

### verify tools ###
/cygdrive/d/TEMP/ApGPackages/cygwin/bin/patch
/cygdrive/d/TEMP/ApGPackages/cygwin/bin/tar
/cygdrive/d/TEMP/ApGPackages/Java/bin/jar
/cygdrive/d/TEMP/ApGPackages/Java/bin/java
/cygdrive/d/TEMP/ApGPackages/cygwin/bin/cpio

### verify ROM ###
### running ./auto_patcher SmoothROM-v5.2.zip openpdroid aokp
PATH= /cygdrive/d/TEMP/ApGPackages/ap/tmp20130702213138:/cygdrive/d/TEMP/ApGPackages/Java/bin:/cygdrive/d/TEMP/ApGPackages/cygwin/bin:/cygdrive/d/TEMP/ApGPackages/cygwin/usr/sbin

### unzip patch tools ###

### unzip patch patches ###

### probe rom type ###
#### Standard Build Query ####
# VER= v2.9.9
# OS= cygwin 32bit
# VID= 4.2.2
# PID= openpdroid
# MID= JDQ39
# RID= aokp
# ANDR= 4.2
# BDID= 20130617
# DID= grouper
# BID= 20130610
Patches are openpdroid/4.2/aokp/20130610

Current HEAD: eeb794d64a8e76f9f7de2b9b0a1bf88b3912829d Merge branch 'master' of [url]https://github.com/mateor/auto-patcher[/url]
53b4e42d056eebbd87e4f6b2dfd7bf913bb2ac55 versioning
33888649fd0063d63d3cdc21efbce69d92d89a9c Merge pull request #135 from Caldair/master
c51126d2da020dc11ca45bf40e56cf8ef6bb6b55 Another tabletUI fix for latest CM Nightlies.

### DELETE FILES=
### COPY FILES= system/media/PDroid.jpeg
### JAR FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar system/framework/telephony-common.jar
### APK FILES= system/app/Mms.apk
### IMG FILES=
### TXT FILES=

### unzip rom ###

### create updater script ###

... using Aroma installer ...
# generated updater-script
ui_print("");
ui_print("");
ui_print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
ui_print("* *");
ui_print("* * The Auto-Patcher * *");
ui_print("* * * * * *");
ui_print("* * by mateor * *");
ui_print("* *");
ui_print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
ui_print("");
ui_print(" Attention");
ui_print(" ************************************");
ui_print("");
ui_print(" There is nothing that can go wrong here");
ui_print(" that reflashing your ROM won't fix.");
ui_print("");
mount("ext4", "EMMC", "/dev/block/platform/sdhci-tegra.3/by-name/APP", "/system");
package_extract_dir("system", "/system");
set_perm_recursive(0, 0, 0755, 0644, "/system");
set_perm_recursive(0, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 02750, "/system/bin/netcfg");
set_perm(0, 3004, 02755, "/system/bin/ping");
set_perm(0, 2000, 06750, "/system/bin/run-as");
set_perm(1002, 1002, 0440, "/system/etc/dbus.conf");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm_recursive(0, 2000, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/etc/init.d");
set_perm(0, 2000, 0550, "/system/etc/init.goldfish.sh");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm(0, 2000, 0755, "/system/vendor");
set_perm(0, 2000, 0755, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/lib");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/lib/drm");
set_perm(0, 0, 0644, "/system/vendor/lib/drm/libdrmwvmplugin.so");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/lib/hw");
set_perm(0, 0, 0644, "/system/vendor/lib/hw/power.grouper.so");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/su");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm_recursive(0, 0, 0755, 0755, "/system/modules");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/bin/fix_permissions");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/addon.d/70-gapps.sh");
set_perm_recursive(0, 0, 0755, 0644, "/system/app");
set_perm(0, 0, 0644, "/system/etc/hosts");
unmount("/system");
ui_print(" .");
ui_print(" .");
ui_print(" done!");

### create restore.zip ###
system\app\Mms.apk : no such file or directory

### decompile system files ###

... decompile framework.jar ...

... extract preloaded-classes ...
inflated: preloaded-classes

... decompile core.jar ...

... decompile services.jar ...

... decompile telephony-common.jar ...
inflated: system/framework/framework-res.apk

... installing framework files ...
### copy patch openpdroid/4.2/aokp/20130610 ###

... copying system/media/PDroid.jpeg ...

... overwriting system/media/PDroid.jpeg from openpdroid ...
`patches/openpdroid/4.2/aokp/20130610/system/media/PDroid.jpeg' -> `./system/media/PDroid.jpeg'

... overwriting ContentResolver.smali ...
### delete patch openpdroid/4.2/aokp/20130610 ###
### jar patch openpdroid/4.2/aokp/20130610 ###

... apply framework.patch ...

... apply preloaded.patch ...
GARBAGE= tmp/system/framework/framework.jar.out/smali/android/hardware/Camera.smali.orig
GARBAGE=

... apply core.patch ...
GARBAGE=
GARBAGE=

... apply services.patch ...

... apply services-gps_fix.patch ...
GARBAGE=
GARBAGE=

... apply telephony-common.patch ...
GARBAGE=
GARBAGE=
### apk patch openpdroid/4.2/aokp/20130610 ###
## No Mms.apk in ROM ###
### img patch openpdroid/4.2/aokp/20130610 ###
### text patch openpdroid/4.2/aokp/20130610 ###

### rebuild jar ###

... rebuild framework.jar ...
adding: classes.dex(in = 8336796) (out= 3368156)(deflated 59%)
adding: preloaded-classes(in = 96019) (out= 16111)(deflated 83%)

... rebuild core.jar ...
adding: classes.dex(in = 2564972) (out= 1072897)(deflated 58%)

... rebuild services.jar ...
adding: classes.dex(in = 2116044) (out= 944501)(deflated 55%)

... rebuild telephony-common.jar ...
adding: classes.dex(in = 1044048) (out= 416128)(deflated 60%)

### rebuild apk ###

### create update-aokp-grouper-20130617-openpdroid.zip ###
added manifest
adding: system/framework/framework.jar(in = 3384852) (out= 3361077)(deflated 0%)
adding: system/framework/core.jar(in = 1076137) (out= 1070169)(deflated 0%)
adding: system/framework/services.jar(in = 944960) (out= 942853)(deflated 0%)
adding: system/framework/telephony-common.jar(in = 416587) (out= 414435)(deflated 0%)
adding: system/media/PDroid.jpeg(in = 26898) (out= 25744)(deflated 4%)
ignoring entry META-INF/
adding: META-INF/com/(in = 0) (out= 0)(stored 0%)
adding: META-INF/com/google/(in = 0) (out= 0)(stored 0%)
adding: META-INF/com/google/android/(in = 0) (out= 0)(stored 0%)
adding: META-INF/com/google/android/update-binary(in = 217728) (out= 141810)(deflated 34%)
adding: META-INF/com/google/android/updater-script(in = 2588) (out= 575)(deflated 77%)

### finished ###

Congratulations, the patching was successful.

Any errors you may have seen were succesfully handled!

!!! Only file a bug report if the software is not behaving as expected !!!

---update-aokp-grouper-20130617-openpdroid.zip

to restore original system, flash:

---restore-aokp-grouper-20130617.zip

updater script

:

ui_print("");
ui_print("");
ui_print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
ui_print("* *");
ui_print("* * The Auto-Patcher * *");
ui_print("* * * * * *");
ui_print("* * by mateor * *");
ui_print("* *");
ui_print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
ui_print("");
ui_print(" Attention");
ui_print(" ************************************");
ui_print("");
ui_print(" There is nothing that can go wrong here");
ui_print(" that reflashing your ROM won't fix.");
ui_print("");
mount("ext4", "EMMC", "/dev/block/platform/sdhci-tegra.3/by-name/APP", "/system");
package_extract_dir("system", "/system");
set_perm_recursive(0, 0, 0755, 0644, "/system");
set_perm_recursive(0, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 02750, "/system/bin/netcfg");
set_perm(0, 3004, 02755, "/system/bin/ping");
set_perm(0, 2000, 06750, "/system/bin/run-as");
set_perm(1002, 1002, 0440, "/system/etc/dbus.conf");
set_perm(1014, 2000, 0550, "/system/etc/dhcpcd/dhcpcd-run-hooks");
set_perm_recursive(0, 2000, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/etc/init.d");
set_perm(0, 2000, 0550, "/system/etc/init.goldfish.sh");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm(0, 2000, 0755, "/system/vendor");
set_perm(0, 2000, 0755, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/lib");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/lib/drm");
set_perm(0, 0, 0644, "/system/vendor/lib/drm/libdrmwvmplugin.so");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/lib/hw");
set_perm(0, 0, 0644, "/system/vendor/lib/hw/power.grouper.so");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 0, 06755, "/system/xbin/su");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm_recursive(0, 0, 0755, 0755, "/system/modules");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/bin/fix_permissions");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm(0, 0, 0755, "/system/addon.d/70-gapps.sh");
set_perm_recursive(0, 0, 0755, 0644, "/system/app");
set_perm(0, 0, 0644, "/system/etc/hosts");
unmount("/system");
ui_print(" .");
ui_print(" .");
ui_print(" done!");