[Android Software/Hacking General [Developers Only]] mithrial:
Exemplary I tried again with 7.2.0

The output of the script was:

ubuntu1% ./auto_patcher cm-7.2.0-bravo.zip pdroid cm7
### verify tools ###
### verify ROM ###
### unzip patch tools ###
### unzip patch patches ###
### unzip rom ###
inflated: system/framework/core.jar
inflated: system/framework/framework.jar
inflated: system/framework/services.jar
### create updater script ###
inflated: META-INF/com/google/android/update-binary
inflated: META-INF/com/google/android/updater-script
### using Clockworkmod installer ###
### create restore.zip ###
### decompile framework.jar ###
... extract preloaded-classes ...
### decompile core.jar ###
### decompile services.jar ###
### patch pdroid/cm7/latest ###
### apply framework.patch ###
... apply preloaded.patch ...
### apply core.patch ###
### apply services.patch ###
### rebuild framework.jar ###
### rebuild core.jar ###
### rebuild services.jar ###
### create updater.zip ###
### finished ###
flash update.zip to install the modified
flash restore.zip to restore the original

The log is as follows:

### verify tools ###
/usr/bin/patch
/bin/tar
/usr/bin/jar
/usr/local/java/jdk1.7.0_05/bin/java
### verify ROM ###
# running ./auto_patcher cm-7.2.0-bravo.zip pdroid cm7
### unzip patch tools ###
baksmali.jar
signapk.jar
smali.jar
updatecert.pem
updatekey.pk8
update-template.zip
### unzip patch patches ###
patches/
patches/v6supercharger/
patches/v6supercharger/files.txt
patches/v6supercharger/generic
patches/v6supercharger/cm9/
patches/v6supercharger/cm9/latest
patches/v6supercharger/cm9/20120614/
patches/v6supercharger/cm9/20120614/services.patch
patches/pdroid/
patches/pdroid/common/
patches/pdroid/common/20120506/
patches/pdroid/common/20120506/preloaded.patch
patches/pdroid/common/20120506/core.patch
patches/pdroid/common/latest
patches/pdroid/files.txt
patches/pdroid/generic
patches/pdroid/cm9/
patches/pdroid/cm9/20120601/
patches/pdroid/cm9/20120601/services.patch
patches/pdroid/cm9/20120601/preloaded.patch
patches/pdroid/cm9/20120601/framework.patch
patches/pdroid/cm9/20120601/core.patch
patches/pdroid/cm9/20120506/
patches/pdroid/cm9/20120506/services.patch
patches/pdroid/cm9/20120506/preloaded.patch
patches/pdroid/cm9/20120506/framework.patch
patches/pdroid/cm9/20120506/core.patch
patches/pdroid/cm9/latest
patches/pdroid/cm9/20120615/
patches/pdroid/cm9/20120615/services.patch
patches/pdroid/cm9/20120615/preloaded.patch
patches/pdroid/cm9/20120615/framework.patch
patches/pdroid/cm9/20120615/core.patch
patches/pdroid/cm9/20120508/
patches/pdroid/cm9/20120508/services.patch
patches/pdroid/cm9/20120508/preloaded.patch
patches/pdroid/cm9/20120508/framework.patch
patches/pdroid/cm9/20120508/core.patch
patches/pdroid/aosp/
patches/pdroid/aosp/20120506/
patches/pdroid/aosp/20120506/services.patch
patches/pdroid/aosp/20120506/preloaded.patch
patches/pdroid/aosp/20120506/framework.patch
patches/pdroid/aosp/20120506/core.patch
patches/pdroid/aosp/20120507/
patches/pdroid/aosp/20120507/services.patch
patches/pdroid/aosp/20120507/preloaded.patch
patches/pdroid/aosp/20120507/framework.patch
patches/pdroid/aosp/20120507/core.patch
patches/pdroid/aosp/latest
patches/pdroid/aosp/20120515/
patches/pdroid/aosp/20120515/services.patch
patches/pdroid/aosp/20120515/preloaded.patch
patches/pdroid/aosp/20120515/framework.patch
patches/pdroid/aosp/20120515/core.patch
patches/pdroid/aokp/
patches/pdroid/aokp/20120613/
patches/pdroid/aokp/20120613/services.patch
patches/pdroid/aokp/20120613/preloaded.patch
patches/pdroid/aokp/20120613/framework.patch
patches/pdroid/aokp/20120613/core.patch
patches/pdroid/aokp/20120506/
patches/pdroid/aokp/20120506/services.patch
patches/pdroid/aokp/20120506/preloaded.patch
patches/pdroid/aokp/20120506/framework.patch
patches/pdroid/aokp/20120506/core.patch
patches/pdroid/aokp/latest
patches/pdroid/aokp/20120510/
patches/pdroid/aokp/20120510/services.patch
patches/pdroid/aokp/20120510/preloaded.patch
patches/pdroid/aokp/20120510/framework.patch
patches/pdroid/aokp/20120510/core.patch
patches/pdroid/cm7/
patches/pdroid/cm7/20120619/
patches/pdroid/cm7/20120619/services.patch
patches/pdroid/cm7/20120619/preloaded.patch
patches/pdroid/cm7/20120619/framework.patch
patches/pdroid/cm7/20120619/core.patch
patches/pdroid/cm7/latest
patches/pdroid/cm7/20120514/
patches/pdroid/cm7/20120514/services.patch
patches/pdroid/cm7/20120514/preloaded.patch
patches/pdroid/cm7/20120514/framework.patch
patches/pdroid/cm7/20120514/core.patch
patches/pdroid/cm7/patch_patches.tgz
# VID=
# MID=
# RID= cm7
# DID=
# BID= latest
# PID= pdroid
### FILES= system/framework/framework.jar system/framework/core.jar system/framework/services.jar
### unzip rom ###
### create updater script ###
### using Clockworkmod installer ###
# generated updater-script
mount("yaffs2", "MTD", "system", "/system");
package_extract_dir("system", "/system");
unmount("/system");
### create restore.zip ###
added manifest
adding: system/framework/framework.jar(in = 3110469) (out= 3092738)(deflated 0%)
adding: system/framework/core.jar(in = 1862816) (out= 1851866)(deflated 0%)
adding: system/framework/services.jar(in = 684722) (out= 683710)(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 = 194648) (out= 125208)(deflated 35%)
adding: META-INF/com/google/android/updater-script(in = 107) (out= 66)(deflated 38%)
### decompile framework.jar ###
... extract preloaded-classes ...
inflated: preloaded-classes
### decompile core.jar ###
### decompile services.jar ###
### apply framework.patch ###
GARBAGE=
GARBAGE=
... apply preloaded.patch ...
### apply core.patch ###
GARBAGE=
GARBAGE=
### apply services.patch ###
GARBAGE=
GARBAGE=
### rebuild framework.jar ###
adding: classes.dex(in = 6366992) (out= 2624937)(deflated 58%)
adding: preloaded-classes(in = 65633) (out= 11974)(deflated 81%)
### rebuild core.jar ###
adding: classes.dex(in = 3586416) (out= 1500973)(deflated 58%)
### rebuild services.jar ###
adding: classes.dex(in = 1278532) (out= 580006)(deflated 54%)
### create updater.zip ###
added manifest
adding: system/framework/framework.jar(in = 2637496) (out= 2619729)(deflated 0%)
adding: system/framework/core.jar(in = 1524013) (out= 1514315)(deflated 0%)
adding: system/framework/services.jar(in = 580465) (out= 579823)(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 = 194648) (out= 125208)(deflated 35%)
adding: META-INF/com/google/android/updater-script(in = 107) (out= 66)(deflated 38%)