I am reluctant to make astshim depend on base (though I will do that if it's necessary for astshim docs to be found). Meanwhile I set EXTRACT_ALL = YES and replaced the use of EXCLUDE_PATTERNS with EXCLUDE += src. If even EXCLUDE contaminates other packages then I'll remove that – it doesn't do any harm to let Doxygen scan the .cc files.

Can you say why you don't want to depend on base? I thought giving all Stack packages shared settings was exactly what that package was for.

From my point of view, astshim could become the standard C++ wrapper for the AST library so I'd like to minimize dependencies on LSST infrastructure.

So astshim is not really a Stack package, and not really an external package?

In any case, I think EXCLUDE += src will have the same side effects on full-Stack builds, but I think I came up with a config that won't clash with other packages. Feel free to merge after replacing or removing that line.

In my view astshim is a 3rd party package so I am reluctant to bring base in.

As per your excellent suggestion I used EXCLUDE_PATTERNS=/astshim/src/.cc". Safe and simple. I also added a pattern for the detail subdirectory, As you said, there's no real need to hide the source; none of it causes Doxygen any problems. But I feel safer keeping it out of the source files.