What I have done is I have taken the class-files from my eclipse project and run them trough an optimizer/obfuscator. So I now have optimized class-files that I want to get
you can try to put them in bin/classes and then use "ant" command to build your application
cd /path/to/my/app
ant release
it will ask you every time for your private key to sign the app, it can be configured to auto-sign by editing "build.properties" file:
key.store=release.keystore
key.alias=release
key.store.password=my_key_password
key.alias.password=my_key_password
you can also investigate Android SDK, find the ANT build scripts it actually uses, and insert your custom obfuscator/optimizer call in middle of build process.
Here's an example:
android create project \
--target 1 \
--name MyAndroidApp \
--path ./MyAndroidAppProject \
--activity MyAndroidAppActivity \
--package com.example.myandroid