apktool decompile when added external java package

Question

I have an android .apk that decompile with apktool with 3rd party program for changing assets and AndroidManifest.XML this is the command for decompiling:
apktool d someAPK.apk somefolder
Now i added an external java package .jar to .apk project with eclips. The external .jar add two directory to my root of apk package(com, coordsys).

When i decompile this new apk with 3rd party program the new directories not appear in the extracted folder.

I dont know should i change the apktool parameter or i should change my method to adding external java package .jar.

Can anybody help me what should i do?

Answer 1

I realized that when i recompile apk with command:
apktool b somfolder someAPK.apk
apktool recreate folders and reorder files in new folders with new names.