At present one has to do a find on all the  .java files in order to process them using javadoc. One typically could use "find . -name *.java -print | xargs javadoc <options>" to traverse the directory tree. This is not a cross-platform solution.

There is definitely a need for a capability of javadoc to traverse the directory tree as one of its options. This will eliminate the need for all the java source to be in one directory.