JRX does not handles multiple top level classes (this bug is not about inner classes) defined in one source file :
- a link is set on the first class defined in the file that point to $(className).html which doesn't exist if the class is not public (so the source file is not $(className).java).
- other classes of the file are not linked. In particular, the public class may not be linked.
- in the class list, some links point ton non-existent files.
Quickfix: ignore all non-public classes.
Long term fix: link all classes. However, this requires to analyse all sources to build the map class->source-file before generating any HTML file.