Android OS uses a Java-based virtual machine called the Dalvik Virtual Machine. A deodexed or .dex file contains the cache used by this virtual machine (referred to as Dalvik-cache) for a program, and it is stored inside the APK. An .odex file, on the other hand, is an optimized version of this same .dex file that is stored next to the APK as opposed to inside it. Android applies this technique by default to all the system applications.
When an Android-based system is booting, the davlik cache for the Davlik VM is built using these .odex files, allowing the OS to learn in advance what applications will be loaded, and thus speeds up the booting process.
By deodexing these APKs, a developer actually puts the .odex files back inside their respective APK packages. Since all code is now contained within the APK itself, it becomes possible to modify any application package without conflicting with the operating system’s execution environment.
Deodex ROMs with jbart
Deodexer is jbart feature that uses smali, baksmali, oat2dex tools to deodex apk and jar files in selected ROM.