[Android Software/Hacking General [Developers Only]] pippodream:
this is my log

ROOT= /home/davide/htc/autopatcherv2.8.7
TOOL= /home/davide/htc/autopatcherv2.8.7/patch_tools.tgz
ROM= /home/davide/htc/autopatcherv2.8.7/cm-10.1-20130328-Albinoman887-pyramid.zip
ROMX= /home/davide/htc/autopatcherv2.8.7/cm-10.1-20130328-Albinoman887-pyramid.zip

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

### verify ROM ###
### running ./auto_patcher cm-10.1-20130328-Albinoman887-pyramid.zip openpdroid cm
PATH= /home/davide/htc/autopatcherv2.8.7/tmp20130328112256:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/android-sdk/tools:/usr/share/java/apache-ant/bin:/home/davide/.cinstall/launchers/:/usr/bin/vendor_perl:/usr/bin/core_perl

### unzip patch tools ###

### unzip patch patches ###

### probe rom type ###
#### Standard Build Query ####
# VER= v2.8.7
# OS= linux-gnu 64bit
# VID= 4.2.2
# PID= openpdroid
# MID= cm_pyramid-userdebug
# RID= cm
# ANDR= 4.2
# BDID= 20130328
# DID= pyramid
# BID= 20130219
Patches are openpdroid/4.2/cm/20130219
### 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/mmcblk0p22", "/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_recursive(0, 2000, 0755, 0644, "/system/vendor/lib");
set_perm(0, 0, 0644, "/system/vendor/lib/libbt-vendor.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");
ui_print(" .");
ui_print(" .");
ui_print(" done!");

### create restore.zip ###

### decompile system files ###

... decompile framework.jar ...

... extract preloaded-classes ...
\decompresso: preloaded-classes

... decompile core.jar ...

... decompile services.jar ...

... decompile telephony-common.jar ...
\decompresso: 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: /home/davide/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/cm/20130219 ###

... copying system/media/PDroid.jpeg ...
"patches/openpdroid/4.2/cm/20130219/system/media/PDroid.jpeg" -> "./system/media/PDroid.jpeg"

... overwriting ContentResolver.smali ...
### delete patch openpdroid/4.2/cm/20130219 ###
### jar patch openpdroid/4.2/cm/20130219 ###

... apply framework.patch ...
1 out of 1 hunk FAILED -- saving rejects to file 'smali/android/app/ContextImpl$42.smali.rej'
1 out of 1 hunk FAILED -- saving rejects to file 'smali/android/app/ContextImpl$43.smali.rej'
1 out of 1 hunk FAILED -- saving rejects to file 'smali/android/app/ContextImpl$44.smali.rej'
2 out of 13 hunks FAILED -- saving rejects to file smali/android/app/ContextImpl.smali.rej
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file smali/android/app/WallpaperInfo.smali.rej

... apply preloaded.patch ...

!!! PATCHING FAILED FOR android/app/ContextImpl$42.smali' android/app/ContextImpl$43.smali' android/app/ContextImpl$44.smali' android/app/ContextImpl.smali !!!
!!! patch error for android/app/ContextImpl$42.smali' !!!

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

!!! error: failed android/app/ContextImpl$42.smali' in framework.jar cannot be remedied

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

anyway, thank you for your tool!