[Android Software/Hacking General [Developers Only]] inh:
EDIT: I guess this doesnt work because Mako isnt in AOSP? According to first post: "Mako support for AOKP and Cm10.1, not stock (b/c Nexus4 is not supported by AOSP, thats the issue here)" although it seems that we could almost get it to work, it's just two failed patched. Let me know if you need anything :)

Can't patch jdq39 when converted to a zip and deodexed using android kitchen I get this error every time:

ROOT= /home/inh/Downloads/ROMs/auto-patcher
TOOL= /home/inh/Downloads/ROMs/auto-patcher/patch_tools.tgz
ROM= /home/inh/Downloads/ROMs/auto-patcher/mako_unsigned_021713_212006.zip
ROMX= /home/inh/Downloads/ROMs/auto-patcher/mako_unsigned_021713_212006.zip

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

### verify ROM ###
### running ./auto_patcher mako_unsigned_021713_212006.zip openpdroid
PATH= /home/inh/Downloads/ROMs/auto-patcher/tmp20130217212310:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/inh/scripts:/home/inh/usr/bin:/home/inh/usr/opt/android-sdk-linux/tools:/home/inh/usr/opt/android-sdk-linux/platform-tools:/usr/lib/go/bin:/home/inh/usr/opt/fdroidserver:/home/inh/projects/go/bin:/home/inh/go/bin:/home/inh/usr/opt/node/bin

### unzip patch tools ###

### unzip patch patches ###

### probe rom type ###
#### Standard Build Query ####
# VER= v2.7.5
# OS= linux-gnu 64bit
# VID= 4.2.2
# PID= openpdroid
# MID= JDQ39
# RID= aosp
# ANDR= 4.2
# BDID= 20130209
# DID= mako
# BID= 20130201
Patches are openpdroid/4.2/aosp/20130201
### 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 system/framework/telephony-common.jar
### APK FILES=
### IMG FILES=
### TXT FILES=

### unzip rom ###

### create updater script ###

... using Clockworkmod 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/mmcblk0p21", "/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_pair_devlist.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_recursive(0, 0, 0755, 0555, "/system/etc/ppp");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor");
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_recursive(0, 2000, 0755, 0755, "/system/xbin");
unmount("/system");
ui_print(" .");
ui_print(" .");
ui_print(" done!");

### create restore.zip ###

### decompile system files ###

... decompile framework.jar ...

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

... decompile core.jar ...

... decompile services.jar ...

... decompile telephony-common.jar ...
### copy patch openpdroid/4.2/aosp/20130201 ###

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

... overwriting system/app/Mms.apk from openpdroid ...
`patches/openpdroid/4.2/aosp/20130201/system/app/Mms.apk' -> `./system/app/Mms.apk'

... copying system/media/PDroid.jpeg ...
`patches/openpdroid/4.2/aosp/20130201/system/media/PDroid.jpeg' -> `./system/media/PDroid.jpeg'
### delete patch openpdroid/4.2/aosp/20130201 ###
### jar patch openpdroid/4.2/aosp/20130201 ###

... apply framework.patch ...
2 out of 14 hunks FAILED -- saving rejects to file smali/android/hardware/Camera.smali.rej
1 out of 23 hunks FAILED -- saving rejects to file smali/android/media/MediaRecorder.smali.rej

... apply preloaded.patch ...

!!! PATCHING FAILED FOR android/hardware/Camera.smali android/media/MediaRecorder.smali !!!
!!! patch error for android/hardware/Camera.smali !!!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!!! error: failed android/hardware/Camera.smali in framework.jar cannot be remedied

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!