I'm gonna add this to the OP for assembling/disassembling .jar files.
smali - An assembler/disassembler for Android's dex format - Google Project Hosting
Using Smali/Baksmali, I will use framework.jar as the example:
-open deodexed framework.jar w/ 7zip, extract classes.dex
-copy classes.dex to your Baksmali folder
-decompile classes.dex (
java -jar baksmali.jar classes.dex)
-make your smali changes in the Out folder
-copy out folder to Smali dir
-compile classes.dex (
java -jar smali.jar -o classes.dex out/)
-copy the new classes.dex to framework.jar