Note, I am not doing this way anymore. I do not know what is the reason you want to do this.
Now I am using just the default asset structure from Paul’s template gradle project. One asset.jar for all of my assets and using runtime files('assets') in build.gradle.
Edit:
I am posting my new approach in case:
I found that getdown already has a mechanism for this by generating patch file, which I think I am going to use this instead of writing my own patcher.