I am not familiar with doxygen or javadoc, but Pod is easy enough to convert to HTML.

My guess it that doxygen or javadoc do some sort of static source code analysis as well? Such a thing is hard to do well in perl, as variables and methods can be created dynamically at runtime using eval. The perl profiler has the ability to display the function call tree after a run, which may provide a start in developing a hierarchical search structure.

Update: fixed a typo.