To better understand deodex, you first need to know about odex.
Stock Android implements an odex file structure, with odex meaning “optimized” dalvik executable file. As your likely aware, Android apps on your device are packaged as .apk files. That all being said, what this means is that for pretty much all of your apks there is a corresponding odex file. This goes for the framework files in .jar format as well.
For instance, on this non-rooted Galaxy Nexus you’ll find
system/app/Phone.apk
as well as
system/app/Phone.odex"
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