[Android Software/Hacking General [Developers Only]] xMemphisx:
Pastebin: http://pastebin.com/JnXycfsm

Log:

ROOT= /Users/qt92160/Downloads/autopatcherv2.1.0/.
TOOL= /Users/qt92160/Downloads/autopatcherv2.1.0/./patch_tools.tgz
ROM= /Users/qt92160/Downloads/autopatcherv2.1.0/bigxie_maguro_OTA_JRO03C_odexed-signed (1).zip
ROMX= /Users/qt92160/Downloads/autopatcherv2.1.0/bigxie_maguro_OTA_JRO03C_odexed-signed (1).zip

### verify tools ###
/usr/bin/patch
/usr/bin/tar
/usr/bin/jar
/usr/bin/java
/usr/bin/cpio

### verify ROM ###
# running ./auto_patcher bigxie_maguro_OTA_JRO03C_odexed-signed (1).zip pdroid aosp-jb 2012.09.02
PATH= /Users/qt92160/Downloads/autopatcherv2.1.0/./tmp20120920213008:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

### unzip patch tools ###
x aapt
x apktool.jar
x baksmali.jar
x signapk.jar
x smali.jar
x updatecert.pem
x updatekey.pk8
x update-template.zip
x boot/
x boot/unpackbootimg
x boot/mkbootimg
x boot/mkbootfs
x cygwin/
x cygwin/mkbootimg.exe
x cygwin/mkbootfs.exe
x cygwin/unpackbootimg.exe
x cygwin/aapt.exe

### unzip patch patches ###
# VID=
# MID=
# RID= aosp-jb
# DID=
# BID= 2012.09.02
# PID= pdroid
### DELETE FILES=
### COPY FILES= system/framework/framework2.jar
### JAR FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### APK FILES=
### IMG FILES= boot.img
### 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, 2000, 0755, 0755, "/system/bin");
set_perm(0, 3003, 06755, "/system/bin/ip");
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(0, 2000, 0550, "/system/etc/init.goldfish.sh");
set_perm(0, 0, 06755, "/system/bin/su");
set_perm_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
set_perm_recursive(0, 2000, 0755, 0755, "/system/vendor/bin");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/etc");
set_perm_recursive(0, 0, 0755, 0644, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/firmware");
set_perm(0, 2000, 0755, "/system/vendor/lib");
set_perm(0, 2000, 0755, "/system/vendor/lib/egl");
set_perm(0, 2000, 0755, "/system/vendor/lib/hw");
set_perm_recursive(0, 2000, 0755, 0755, "/system/xbin");
set_perm(0, 1000, 0755, "/system/xbin/busybox");
unmount("/system");
package_extract_file("boot.img", "/dev/block/platform/omap/omap_hsmmc.0/by-name/boot");

### create restore.zip ###
added manifest
adding: system/framework/framework.jar(in = 14961) (out= 14800)(deflated 1%)
adding: system/framework/core.jar(in = 4124) (out= 3386)(deflated 17%)
adding: system/framework/services.jar(in = 313) (out= 178)(deflated 43%)
adding: boot.img(in = 4470784) (out= 4450012)(deflated 0%)
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 = 249144) (out= 156325)(deflated 37%)
adding: META-INF/com/google/android/updater-script(in = 1617) (out= 408)(deflated 74%)

### decompile system files ###

... decompile framework.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.DexFile$NoClassesDexException: zip file framework.jar does not contain a classes.dex file
at org.jf.dexlib.DexFile.<init>(DexFile.java:298)
at org.jf.baksmali.main.main(main.java:269)

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

... decompile core.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.DexFile$NoClassesDexException: zip file core.jar does not contain a classes.dex file
at org.jf.dexlib.DexFile.<init>(DexFile.java:298)
at org.jf.baksmali.main.main(main.java:269)

... decompile services.jar ...

UNEXPECTED TOP-LEVEL EXCEPTION:
org.jf.dexlib.DexFile$NoClassesDexException: zip file services.jar does not contain a classes.dex file
at org.jf.dexlib.DexFile.<init>(DexFile.java:298)
at org.jf.baksmali.main.main(main.java:269)

### unpacking boot.img ###
./auto_patcher: line 516: ./unpackbootimg: cannot execute binary file
0 blocks

### copy patch pdroid/aosp-jb/latest ###

... copying system/framework/framework2.jar ...

### jar patch pdroid/aosp-jb/latest ###

... apply framework.patch ...

... apply preloaded.patch ...

... apply core.patch ...

... apply services.patch ...

### img patch pdroid/aosp-jb/latest ###