[Android Software/Hacking General [Developers Only]] harlequin69:
Teething problems are always going to occur we are all grateful that you do this for us at all :)

Still failed from command line after script and I also tried Kobiks new ApG and it failed also, sorry to keep bugging you with this.

ROOT= /cygdrive/d/Neil/Desktop/ApG/ApGPackages/ap/
TOOL= /cygdrive/d/Neil/Desktop/ApG/ApGPackages/ap//patch_tools.tgz
ROM= /cygdrive/g/goomanager/pa_grouper-2.50-23OCT2012-143124.zip
ROMX= G:\GOOMAN~1\PA_GRO~4.ZIP

### verify tools ###
/cygdrive/d/Neil/Desktop/ApG/ApGPackages/cygwin/bin/patch
/cygdrive/d/Neil/Desktop/ApG/ApGPackages/cygwin/bin/tar
/cygdrive/d/Neil/Desktop/ApG/ApGPackages/Java/bin/jar
/cygdrive/d/Neil/Desktop/ApG/ApGPackages/Java/bin/java
/cygdrive/d/Neil/Desktop/ApG/ApGPackages/cygwin/bin/cpio

### verify ROM ###
### running ./auto_patcher /cygdrive/g/goomanager/pa_grouper-2.50-23OCT2012-143124.zip extension,v6supercharger
PATH= /cygdrive/d/Neil/Desktop/ApG/ApGPackages/ap/tmp20121024095654:/cygdrive/d/Neil/Desktop/ApG/ApGPackages/Java/bin:/cygdrive/d/Neil/Desktop/ApG/ApGPackages/cygwin/bin:/cygdrive/d/Neil/Desktop/ApG/ApGPackages/cygwin/usr/sbin

### unzip patch tools ###

### unzip patch patches ###

### probe rom type ###
# VER= Auto-Patcher v2.2.02
# OS= cygwin 32bit
# VID= 4.1.2
# PID= extension v6supercharger
# MID= pa_grouper-userdebug
# RID= pa
# ANDR= jellybean
# BDID=
# DID= grouper
# BID= latest
### DELETE FILES=
### COPY FILES= system/media/PDroid.jpeg
### JAR FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### APK FILES= system/app/Mms.apk
### IMG FILES=
### TXT FILES=

### unzip rom ###

### create updater script ###

... using Clockworkmod installer ...
# generated updater-script
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, 0, 0755, 0755, "/system/addon.d");
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_recursive(1002, 1002, 0755, 0440, "/system/etc/bluetooth");
set_perm(0, 0, 0755, "/system/etc/bluetooth");
set_perm(1000, 1000, 0640, "/system/etc/bluetooth/auto_pairing.conf");
set_perm(3002, 3002, 0444, "/system/etc/bluetooth/blacklist.conf");
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(1000, 1000, 0644, "/system/etc/paranoid/properties.conf");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm(0, 2000, 0755, "/system/vendor");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/etc");
set_perm(0, 0, 0644, "/system/vendor/etc/audio_effects.conf");
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/librank");
set_perm(0, 0, 06755, "/system/xbin/procmem");
set_perm(0, 0, 06755, "/system/xbin/procrank");
set_perm(0, 0, 06755, "/system/xbin/su");
unmount("/system");

### 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 Mms.apk ...

### copy patch extension/jellybean/pa/latest ###

... copying system/media/PDroid.jpeg ...
`patches/extension/jellybean/pa/latest/system/media/PDroid.jpeg' -> `./system/media/PDroid.jpeg'

### jar patch extension/jellybean/pa/latest ###

... apply framework.patch ...
1 out of 5 hunks FAILED -- saving rejects to file smali/com/android/internal/telephony/gsm/GsmServiceStateTracker.smali.rej

!!! PATCHING FAILED FOR com/android/internal/telephony/gsm/GsmServiceStateTracker.smali !!!
!!! patch error for com/android/internal/telephony/gsm/GsmServiceStateTracker.smali !!!
askconsent intial = yes
askconsent final = yes: for com/android/internal/telephony/gsm/GsmServiceStateTracker.smali

... replace com/android/internal/telephony/gsm/GsmServiceStateTracker.smali ...
`patches/extension/jellybean/provisionals/system/framework/framework.jar.out/smali/com/android/internal/telephony/gsm/GsmServiceStateTracker.smali' -> `tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/gsm/GsmServiceStateTracker.smali'
GARBAGE=
GARBAGE=

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

... apply services.patch ...
GARBAGE=
GARBAGE=

### apk patch extension/pa/latest ###
## No Mms.apk in ROM ###

### jar patch v6supercharger/jellybean/generic/latest ###

... apply services.patch ...
GARBAGE= tmp/system/framework/services.jar.out/smali/com/android/server/am/ProcessList.smali.orig
GARBAGE=

### rebuild jar ###

... rebuild framework.jar ...
adding: classes.dex(in = 8839656) (out= 3576823)(deflated 59%)
adding: preloaded-classes(in = 84422) (out= 14499)(deflated 82%)

... rebuild core.jar ...
adding: classes.dex(in = 2512092) (out= 1045815)(deflated 58%)

... rebuild services.jar ...
adding: classes.dex(in = 1817392) (out= 815805)(deflated 55%)

### rebuild apk ###

... rebuild Mms.apk ...
Exception in thread "main" brut.androlib.AndrolibException: brut.directory.DirectoryException: java.io.FileNotFoundException: tmp\system\app\Mms.apk.out (The system cannot find the path specified)
at brut.androlib.Androlib.readMetaFile(Androlib.java:162)
at brut.androlib.Androlib.build(Androlib.java:179)
at brut.androlib.Androlib.build(Androlib.java:174)
at brut.apktool.Main.cmdBuild(Main.java:188)
at brut.apktool.Main.main(Main.java:70)
Caused by: brut.directory.DirectoryException: java.io.FileNotFoundException: tmp\system\app\Mms.apk.out (The system cannot find the path specified)
at brut.directory.ZipRODirectory.<init>(ZipRODirectory.java:55)
at brut.directory.ZipRODirectory.<init>(ZipRODirectory.java:38)
at brut.androlib.res.util.ExtFile.getDirectory(ExtFile.java:55)
at brut.androlib.Androlib.readMetaFile(Androlib.java:158)
... 4 more
Caused by: java.io.FileNotFoundException: tmp\system\app\Mms.apk.out (The system cannot find the path specified)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:214)
at java.util.zip.ZipFile.<init>(ZipFile.java:144)
at java.util.zip.ZipFile.<init>(ZipFile.java:158)
at brut.directory.ZipRODirectory.<init>(ZipRODirectory.java:53)
... 7 more

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