I\'ve set up my project in Android Studio to use the Square Wire library, as per this question.
Build -> Compile Project works fine.
It seems that everyone uses a different approach for getting around these issues. I'll suggest another one that I feel is a bit less invasive than the others. When I introduce changes from an aar library that I include, I will open up the "settings.gradle" file for the project.
Then cut out the main project module from the list of projects:
include ':mainproj',
and then sync your project. Then paste it back in and re-sync your project once more. I believe that this is the same as some of the manual deletion steps, but this lets you do so from the IDE a bit quicker and less painfully.