Simply grab your rom or theme and place it in this folder (should work from anywhere but you need to full path from where the cmd file is run). Now click on the reopto_runner.cmd and it will ask you where the rom is (name) that you want to optomize, type the name of the rom and hit enter, it will do the rest.
Final output of the re-optimized (double pass with 2 different png optimizers) rom will be named rom-optoed-signed-finished.zip this will be exactly the same rom except the script will optomize every png in every apk found in the system/app and system/framework-res.apk. It will also zipalign all these same apks and finally will sign the zip file. When its done just rename the rom-optoed-signed-finished.zip to what ever you want and its ready to flash.
What this won't do is make your zip file (rom, theme, update zip) flashable unless its already set up to be flashable... meaning you'll still need your update-script in the com.google.android folder to be there. Its does sign your zip file for you though.
I put this out there as its some of the scripting and tools I have made to help me in theming and rom hacking.
Feel free to use any part of this to help you in any scripting you do.