With JSR199, it is reasonable to set locations directly on the file manager, rather than going via the compiler's option processing code. If you do, JavacProcessingEnvironment does not pick up the correct values for the processor path and class path, because it assumes they will be set via options.

This is because of the following...
-- JavacProcessingEnvironment.java, line 189
if ((postfixPath = options.get("-processorpath")) == null )
if ((postfixPath = options.get("-classpath")) == null )
postfixPath = ".";
-- DefaultFileManager.java
      handleOptions propogates its options into the main option table, but
      setLocation does not propogate locations to the main option table.