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if you are developing and documenting a library.. do you document every single function / data structure from every source file, or just the public ones that appear on the public header??
im leaning to the second option, is this ok?
The answer to your question depends on who is going to read the documentation. If the documentation is going to users of your API, it is probably better that you only provided them with documentation for the public interface. As this way they will not be overwhelmed by details that are not relevant to them.
On the other hand if your documentation is to be read by people maintaining the library, it should include documentation on both the public and private code.
Right now I am using a slightly different approach to arne. I have a script which copies the header files needed for the public interface to a separate directory for packaging up. This is necessary anyway for producing releases. The script also copies the Doxyfile configuration to that directory and then runs doxygen on the reduced set of files. That way I have one doxygen configuration file that I use to produce both public and private documentation.