It's been a while since I used DOXYGEN (probably 15 years+ :)), but have you tried DOXYGEN with EXAMPLE_RECURSIVE tag? I am with the impression it did quite an excellent job in these days (talk 2000-2002).
EXAMPLE_RECURSIVE If the EXAMPLE_RECURSIVE tag is set to YES then
subdirectories will be searched for input files to be used with the
\include or \...
If you need one IDE for multiple languages then a good bet is Eclipse is supports almost every programming language and multiple platforms with plugins for many languages, (it also has the user interface supporting 44 or more human languages).
It is available free and is licenced under the Eclipse Public
Supports multiple tool chains for the ...