AA uses processingEnv.getMessager() to log some information during processing. But sometimes IDEs can't shows this messages because they can't be linked to an element. With maven messages are also truncated to few lines. In theses cases we lost relevant information.

To improve debugging and to be sure we have always some logs, it could be interesting to add them in a file with a good old logger using slf4j / logback.
We could configure the output file and debug level with annotation processor options like trace, androidManifestFile and resourcePackageName.

I'll work on this point quickly because it could be very helpful during 3.0 release process :)