Processing annotations without clean/compile?

Question

I am trying to process all classes that have an @Entity annotation, creating a list of these to be used in another part of the application. Because the annotation processor uses javac, it only seems to work on files that have changed. So, without either cleaning the output dir or touching all input files, the processor will find all @Entity annotated-classes the first time, but only changed ones on future runs. This means I cannot guarantee a complete list every run (without resorting to clean or touch, but that's not an acceptible solution because it is much slower).
Some questions:
1. Is the annotation processor only able to work on files that appear changed? This seems like bad design for the processor which is suppose to work with source code (i.e. it shouldn't care whether the class file is out-of-date, it should always process whatever source is there).
2. Is there a better way to find all classes with a given annotation? Either at compile time or at runtime?

Answer 1

I'm not a dev, but for what it's worth:
I ran across almost the same case myself, and I imagine that the correct course is to maintain that list of annotations to be used elsewhere in a separate resource file, which would be generated on the first run and subsequently updated with whatever annotations the processor sees on those runs. My own processor is supposed to (that part is broken for now) use roughly this method for caching metadata gathered from an external source at annotation-processing time, by maintaining an .xml file that contains a "complete picture" of things.
If there is more to it then I've missed something and I'm very eager to hear what that might be.