Code2Doc bother

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I'm having trouble using Cod2Doc.
I can get it to create the documentation for my program, but it contains a number of includes in a subdirectory.
The program appears to notice this and operate appropriately with them, because it will list the includes with the proper links (to a subdirectory) in the actual documentation. However, it does not create documentation for these includes, and so all of those links are broken.
I'm hoping that there is a setting which I am missing.