What is the proper method of including an entire Documentation folder for companion guides but still having the files end up in docs?
At present it seems that if you use --include folder it will always create a folder under docs for that messing up the back link to index as reported in #324.
The problem seems to be that appledoc should not try to preserve the folder, but only subfolders of a project. Or have an option to force appledoc to flatten the hierarchy.
This was actually intended so (if I understand correctly), so that all companion files would be embedded inside a folder, not scattered among the rest of the files (potentially overwriting one of the generated ones). The whole documents thing should work as described here. Seems like output is generated that way, it's just links that are broken, as you describe on #324?