[Android Software/Hacking General [Developers Only]] mithrial:
The newest version still bootloops for me.

Output:

ubuntu1% ./auto_patcher cm-7-20120624-NIGHTLY-bravo.zip pdroid cm7 20120618
### 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/cm7/20120618 ###
### apply framework.patch ###
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file smali/com/android/internal/telephony/cdma/EriManager.smali.rej
### 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

Log (unzip stripped for better readability):

### verify tools ###
/usr/bin/patch
/bin/tar
/usr/bin/jar
/usr/bin/java
### verify ROM ###
# running ./auto_patcher cm-7-20120624-NIGHTLY-bravo.zip pdroid cm7 20120618
### unzip patch tools ###
baksmali.jar
signapk.jar
smali.jar
updatecert.pem
updatekey.pk8
update-template.zip
### unzip patch patches ###
...
# VID=
# MID=
# RID= cm7
# DID=
# BID= 20120618
# 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 = 3111222) (out= 3093059)(deflated 0%)
adding: system/framework/core.jar(in = 1862816) (out= 1851861)(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 = 194664) (out= 125211)(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 ###
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file smali/com/android/internal/telephony/cdma/EriManager.smali.rej
GARBAGE= tmp/system/framework/framework.jar.out/smali/com/google/android/mms/pdu/PduPersister.smali.orig
GARBAGE= tmp/system/framework/framework.jar.out/smali/com/android/internal/telephony/cdma/EriManager.smali.rej
### apply core.patch ###
GARBAGE=
GARBAGE=
### apply services.patch ###
GARBAGE=
GARBAGE=
### rebuild framework.jar ###
adding: classes.dex(in = 6369596) (out= 2625766)(deflated 58%)
adding: preloaded-classes(in = 65520) (out= 11935)(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 = 2638286) (out= 2620674)(deflated 0%)
adding: system/framework/core.jar(in = 1524013) (out= 1514315)(deflated 0%)
adding: system/framework/services.jar(in = 580465) (out= 579822)(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 = 194664) (out= 125211)(deflated 35%)
adding: META-INF/com/google/android/updater-script(in = 107) (out= 66)(deflated 38%)