[Android Software/Hacking General [Developers Only]] asicman:
mateorod, please see the following:

### verify ROM ###
### running ./auto_patcher pa_maguro-2.51-24OCT2012-161109.zip pd2.0 pa
PATH= /cygdrive/c/Users/shiv/Desktop/gingerbread/JB/ApGPackages/ap/tmp20121027002904:/cygdrive/c/Users/shiv/Desktop/gingerbread/JB/ApGPackages/Java/bin:/cygdrive/c/Users/shiv/Desktop/gingerbread/JB/ApGPackages/cygwin/bin:/cygdrive/c/Users/shiv/Desktop/gingerbread/JB/ApGPackages/cygwin/usr/sbin

### unzip patch tools ###

### unzip patch patches ###

### probe rom type ###
#### Standard Build Query ####
# VER= Auto-Patcher v2.3.0
# OS= cygwin 32bit
# VID= 4.1.2
# PID= pd2.0
# MID= pa_maguro-userdebug
# RID= pa
# ANDR= jellybean
# BDID= 20121024
# DID= maguro
# BID= 20121016
### DELETE FILES=
### COPY FILES= system/app/Mms.apk system/media/PDroid.jpeg
### JAR FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### APK FILES=
### IMG FILES=
### TXT FILES=

### unzip rom ###

### create updater script ###

... using Clockworkmod installer ...
# generated updater-script
mount("ext4", "EMMC", "/dev/block/platform/omap/omap_hsmmc.0/by-name/system", "/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, 0755, "/system/vendor/bin");
set_perm(0, 2000, 0755, "/system/vendor/etc");
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(0, 2000, 0755, "/system/vendor/lib/egl");
set_perm(0, 2000, 0755, "/system/vendor/lib/hw");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/res");
set_perm(0, 0, 0644, "/system/vendor/res/images/dock/dock.png");
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 ###

### decompile system files ###

... decompile framework.jar ...

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

... decompile core.jar ...

... decompile services.jar ...

### copy patch pd2.0/jellybean/pa/20121016 ###

... copying system/app/Mms.apk ...

... overwriting system/app/Mms.apk from pd2.0 ...
`patches/pd2.0/jellybean/pa/20121016/system/app/Mms.apk' -> `./system/app/Mms.apk'

... copying system/media/PDroid.jpeg ...
`patches/pd2.0/jellybean/pa/20121016/system/media/PDroid.jpeg' -> `./system/media/PDroid.jpeg'

### jar patch pd2.0/jellybean/pa/20121016 ###

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

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

... replace com/android/internal/telephony/gsm/GsmServiceStateTracker.smali ...
`patches/pd2.0/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=

### rebuild jar ###

... rebuild framework.jar ...
adding: classes.dex(in = 8840084) (out= 3577192)(deflated 59%)
adding: preloaded-classes(in = 84422) (out= 14499)(deflated 82%)

... rebuild core.jar ...
tmp\system\framework\core.jar.out\smali\java\util\prefs\FilePreferencesImpl.smali[0,0] Must call setParent before comparing AnnotationDirectoryItem instances

Do you want to proceed ? (YES/no) yes
... replace com/android/internal/telephony/gsm/GsmServiceStateTracker.smali ...
... apply core.patch ...
... apply services.patch ...
### rebuild jar ###
... rebuild framework.jar ...
... rebuild core.jar ...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! error: failed compiling core.jar !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

! please refer to /cygdrive/c/Users/shiv/Desktop/gingerbread/JB/ApGPackages/ap/l
og20121027002904.txt for any debugging

! patching failed.
! it may be possible to patch /cygdrive/c/Users/shiv/Desktop/gingerbread/JB/ApGP
ackages/ap/pa_maguro-2.51-24OCT2012-161109.zip using other patch version