Even if it is not possible to use proguard for an entire grails app would it be possible to just use it for the src/java folder?
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I don't know either Proguard or Grails in depth, but I do know that:
Thus my intuition is yes, ProGuard can shrink/obfuscate grails apps. Your question asks about using ProGuard on the src/java folder. It's important to understand that ProGuard operates on .class files, not .java files. A correct configuration will need to operate on your bin directory, not src. Unfortunately I'm not qualified to give you a detailed example configuration, but I hope this gets you on the right path.