Tools:

I recommend cloning the git repos so you have the latest versions, as these are mostly beta tools.

Tips:

If you need to debug an application use apktool d file.apk then edit the AndroidManifest.xml file by adding android:debuggable="true" to the application section. After you can use apktool b directory -o newapk.apk to build an apk that you can attach smalidea to.

A good reference for Dalvik opcodes.