[ONE Themes and Apps] Devo7v:
I've gone in to the zip and removed all of the folders under /system except /system/addon.d and /system/priv-app/ThemeChooser.

I modified 01-cyngn.sh from:

#!/sbin/sh
#
# /system/addon.d/01-cyngn.sh
#
. /tmp/backuptool.functions

list_files() {
cat <<EOF
addon.d/01-cyngn.sh
priv-app/AmbientCore/AmbientCore.apk
priv-app/AmbientUpdater/AmbientUpdater.apk
priv-app/AudioFX/AudioFX.apk
priv-app/CMLogger/CMLogger.apk
priv-app/CyanogenStats/CyanogenStats.apk
priv-app/DeviceManager/DeviceManager.apk
priv-app/DialerNext/DialerNext.apk priv-app/Dialer/Dialer.apk
priv-app/DialerNext/ priv-app/Dialer/
priv-app/GalleryNext/GalleryNext.apk
priv-app/Screencast/Screencast.apk
priv-app/ThemeChooser/ThemeChooser.apk
priv-app/ThemeStore/ThemeStore.apk
app/TruecallerCM/TruecallerCM.apk
app/InCallUINext/ app/InCallUI/
app/InCallUINext/InCallUINext.apk app/InCallUI/InCallUI.apk
etc/permissions/com.cyanogen.ambient.xml
etc/permissions/com.cyngn.audiofx.xml
etc/permissions/org.cyanogenmod.partner.boxer.xml
EOF
}

case "$1" in
backup)
list_files | while read FILE DUMMY; do
backup_file $S/$FILE
done
;;
restore)
list_files | while read FILE REPLACEMENT; do
R=""
[ -n "$REPLACEMENT" ] && R="$S/$REPLACEMENT"
[ -f "$C/$S/$FILE" ] && restore_file $S/$FILE $R
done
;;
pre-backup)
# Stub
;;
post-backup)
# Stub
;;
pre-restore)
# Stub
;;
post-restore)
# Stub
;;
esac

And modified it to:

#!/sbin/sh
#
# /system/addon.d/01-cyngn.sh
#
. /tmp/backuptool.functions

list_files() {
cat <<EOF
addon.d/01-cyngn.sh
priv-app/ThemeChooser/ThemeChooser.apk
EOF
}

case "$1" in
backup)
list_files | while read FILE DUMMY; do
backup_file $S/$FILE
done
;;
restore)
list_files | while read FILE REPLACEMENT; do
R=""
[ -n "$REPLACEMENT" ] && R="$S/$REPLACEMENT"
[ -f "$C/$S/$FILE" ] && restore_file $S/$FILE $R
done
;;
pre-backup)
# Stub
;;
post-backup)
# Stub
;;
pre-restore)
# Stub
;;
post-restore)
# Stub
;;
esac

I then went in to the updater-script and modified it from:

ui_print("Installing Cyanogen Apps test package...");
run_program("/sbin/busybox", "mount", "/system");
show_progress(1, 15);
delete("/system/priv-app/AudioFX/AudioFX.apk","/system/priv-app/Dialer/Dialer.apk","/system/app/InCallUI/InCallUI.apk","/system/priv-app/ThemeChooser/ThemeChooser.apk");
delete_recursive("/system/priv-app/Dialer");
delete_recursive("/system/app/InCallUI");
package_extract_dir("system", "/system");
set_perm(0, 0, 0755, "/system/addon.d/01-cyngn.sh");
show_progress(1, 15);
ui_print("Setting metadata...");
set_metadata_recursive("/system/app", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata_recursive("/system/priv-app", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
set_metadata_recursive("/system/etc/permissions", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
run_program("/sbin/busybox", "umount", "/system");
ui_print("Done!");

I've modified it to:

ui_print("Installing Cyanogen Theme Chooser test package...");
run_program("/sbin/busybox", "mount", "/system");
show_progress(1, 15);
delete("/system/priv-app/ThemeChooser/ThemeChooser.apk");
package_extract_dir("system", "/system");
set_perm(0, 0, 0755, "/system/addon.d/01-cyngn.sh");
show_progress(1, 15);
ui_print("Setting metadata...");
set_metadata_recursive("/system/priv-app", "uid", 0, "gid", 0, "dmode", 0755, "fmode", 0644, "capabilities", 0x0, "selabel", "u:object_r:system_file:s0");
run_program("/sbin/busybox", "umount", "/system");
ui_print("Done!");

I'm in the process of making a backup before I flash. Do you think it'll work? Are there any other files I need to modify?