[Soot-list] Instrumenting Android Apk

[H S]

Hi,
I am trying to regenerate this project LINK. 
The only thing I have tried was issuing a command like: 
java -jar soot.jar soot.Main -allow-phantom-refs 
 -android-jars /opt/android-sdk-linux/platforms 
 -src-prec apk
  -process-dir ~/RV2013Examples/exampleApp/RV2013/bin/RV2013.apk 
 -output-format dex
Which gave an new apk in sootOutput directory. 
Now my question is that (1)what are all the steps to this manual Android instrumentation. I read the article of "instrumenting easy as abc", but it was not clear on this. 
(2) What are the usages of files MyBodyTransformer.java, Main.java, and Settings.java, how one should include them in the project? 

Thanks,
Sarah 
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