I am using doxygen for creating JavaDoc for my project. but after running doxygen- all the output files is under the same folder- the output root folder. for example- I have Foo class and in it- A and B structs. What I want is the under the root folder will be folder "Foo" and under the "Foo" folder will be the A and the B structs (in JavaDoc I have it. only in doxygen I dont have it.)
Do you know if there is flag in doxygen that can output the files in folder hierarchy?
No there is no such option.
Question is why is it important how the output is structured if you view it with a browser anyway? You should not really care.
In case you are worried about slow file access due to too many files in one directory you should enable the
CREATE_SUBDIRSoption. This does distribute the files over multiple directories but not in the way you requested it.