[Android Software/Hacking General [Developers Only]] Stylez Ray.:
Could you please have a look at the log?

This is on a Nexus 4 running Xylon ROM. It has never worked to patch for now, I waited for weeks and tried every nightly and used every AP version...

ROOT= /cygdrive/d/AutoPatcherGUI/ApGPackages/ap
TOOL= /cygdrive/d/AutoPatcherGUI/ApGPackages/ap/patch_tools.tgz
ROM= /cygdrive/c/Users/style_000/Desktop/xylon_mako_2.4.2_20130411.zip
ROMX= C:\Users\STYLE_~1\Desktop\XYLON_~1.ZIP

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

### verify ROM ###
### running ./auto_patcher /cygdrive/c/Users/style_000/Desktop/xylon_mako_2.4.2_20130411.zip openpdroid aokp
PATH= /cygdrive/d/AutoPatcherGUI/ApGPackages/ap/tmp20130413080641:/cygdrive/d/AutoPatcherGUI/ApGPackages/Java/bin:/cygdrive/d/AutoPatcherGUI/ApGPackages/cygwin/bin:/cygdrive/d/AutoPatcherGUI/ApGPackages/cygwin/usr/sbin

### unzip patch tools ###

### unzip patch patches ###

### probe rom type ###
#### Standard Build Query ####
# VER= v2.9.1
# OS= cygwin 32bit
# VID= 4.2.2
# PID= openpdroid
# MID= xylon_mako-userdebug
# RID= aokp
# ANDR= 4.2
# BDID= 20130411
# DID= mako
# BID= 20130405
Patches are openpdroid/4.2/aokp/20130405
### 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 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/platform/msm_sdcc.1/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(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_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/firmware/discretix");
set_perm(0, 2000, 0755, "/system/vendor/firmware/keymaster");
set_perm_recursive(0, 2000, 0755, 0644, "/system/vendor/firmware/wlan");
set_perm(0, 0, 0644, "/system/vendor/firmware/wlan/prima/WCNSS_cfg.dat");
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, 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");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/init.d");
set_perm_recursive(0, 0, 0755, 0755, "/system/etc/cron");
unmount("/system");
ui_print(" .");
ui_print(" .");
ui_print(" done!");

### create restore.zip ###

### decompile system files ###

... decompile framework.jar ...

... extract preloaded-classes ...
\vergr�t: preloaded-classes

... decompile core.jar ...

... decompile services.jar ...

... decompile telephony-common.jar ...
\vergr�t: system/framework/framework-res.apk

... installing framework files ...

... decompile Mms.apk ...
I: Baksmaling...
I: Loading resource table...
I: Loaded.
I: Decoding AndroidManifest.xml with resources...
I: Loading resource table from file: C:\Users\style_000\apktool\framework\1.apk
I: Loaded.
I: Regular manifest package...
I: Decoding file-resources...
I: Decoding values */* XMLs...
I: Done.
I: Copying assets and libs...
### copy patch openpdroid/4.2/aokp/20130405 ###

... copying system/media/PDroid.jpeg ...
`patches/openpdroid/4.2/aokp/20130405/system/media/PDroid.jpeg' -> `./system/media/PDroid.jpeg'
### delete patch openpdroid/4.2/aokp/20130405 ###
### jar patch openpdroid/4.2/aokp/20130405 ###

... apply framework.patch ...
The text leading up to this was:
--------------------------
|diff -Npruw stock-framework/smali/android/app/ContextImpl$41.smali opd-framework/smali/android/app/ContextImpl$41.smali
|--- stock-framework/smali/android/app/ContextImpl$41.smali	2013-04-10 19:01:38.283441649 -0500
|+++ opd-framework/smali/android/app/ContextImpl$41.smali	2013-04-10 19:01:28.495393130 -0500
--------------------------
File to patch:
Skip this patch? [y]
1 out of 1 hunk ignored
The text leading up to this was:
--------------------------
|diff -Npruw stock-framework/smali/android/app/ContextImpl$42.smali opd-framework/smali/android/app/ContextImpl$42.smali
|--- stock-framework/smali/android/app/ContextImpl$42.smali	2013-04-10 19:01:38.283441649 -0500
|+++ opd-framework/smali/android/app/ContextImpl$42.smali	2013-04-10 19:01:28.495393130 -0500
--------------------------
File to patch:
Skip this patch? [y]
1 out of 1 hunk ignored
2 out of 11 hunks FAILED -- saving rejects to file smali/android/app/ContextImpl.smali.rej
14 out of 15 hunks FAILED -- saving rejects to file smali/android/app/Fragment.smali.rej
2 out of 3 hunks FAILED -- saving rejects to file 'smali/android/app/LoaderManagerImpl$LoaderInfo.smali.rej'
2 out of 9 hunks FAILED -- saving rejects to file 'smali/android/provider/Settings$Secure.smali.rej'

... apply preloaded.patch ...

!!! PATCHING FAILED FOR android/app/ContextImpl.smali android/app/Fragment.smali android/app/LoaderManagerImpl$LoaderInfo.smali' android/provider/Settings$Secure.smali' !!!
!!! patch error for android/app/ContextImpl.smali !!!

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

!!! error: failed android/app/ContextImpl.smali in framework.jar cannot be remedied

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