The answers are already kind of outdated or not complete. This maybe works for non-protected apks (no Proguard), but nowadays nobody deploys an unprotected apk. The way I was able to modify a (my) well-protected apk (Proguard, security check which checks for "hacking tools", security check, which checks if the app is repackaged with debug mode,...) is via apktool as already mentioned by other ones here. But nobody explained, that you have to sign the app again.
apktool d app.apk
//generates a folder with smali bytecode files.
//Do something with it.
apktool b [folder name] -o modified.apk
//generates the modified apk.
//and then
jarsigner -verbose -sigalg SHA1withRSA -digestalg SHA1 -keystore ~/.android/debug.keystore modified.apk androiddebugkey
//signs the app the the debug key (the password is android)
//this apk can be installed on a device.
In my test, the original release apk had no logging. After I decompiled with apktool I exchanged a full byte code file without logging by a full byte code file with logging, re-compiled and signed it and I was able to install it on my device.
Afterwards I was able to see the logs in Android Studio as I connected the app to it.
In my opinion, decompiling with dex2jar and JD-GUI is only helpful to get a better understanding what the classes are doing, just for reading purposes. But since everything is proguarded, I'm not sure that you can ever re-compile this half-baked Java code to a working apk. If so, please let me know. I think, the only way is to manipulate the byte code itself as mentioned in this example.
