I'm having a problem with Doxygen for Windows with Python where input files with the same failename cause a conflict wth the output files. This seems to be a bug in doxygen - is there a way to work-around this problem?
Background
We build docs for our API using Doxygen. Our project is overwhelmingly written in python and the only components that our clients care about are python. Due to accidents of history our classes often have unfortunate naming conventions.
For example we have a classes whose fully-qualified name are:
tools.b.foo.Foo
tools.b.bar.Bar
Later this class was re-implemented and put into a new module:
tools.c.foo.Foo_improved
tools.c.bar.Bar_improved
When we want to build our tools API documentation we have a process which checks out tools.* into a directory on the build-server and then we call doxygen with a fairly standard configuration file.
We'd expect that there should be four HTML files in the output, two for foo and two for bar. However what we get is only two files. Both sets of sripts are parsed, however since the module names are the same the documentation for the old version ends up over-writing the documentation which was generated for the new versions. As a result in every case where a python module name is duplicated (but in a different sub-package) we are only getting a single doc file for every file name.
FYI, we are using doxygen 1.7.1 on Windows XP 32bit with Python 2.4.4
Config file is here: http://pastebin.me/002f3ec3145f4e1896a9cf79e7179493
UPDATE 1: In the generated doc index I can see entries for all four files, however if I follow the links to both Foo and Foo_improved both point to the same file.
