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Ensure that the package overview HTML does not include prefixes like __AJDECLID:181:__ before each item (see attached example).
Created attachment 9297 [details] example package output with synthetic information
This would show if ajdoc was fun in file mode (i.e. ajdoc <file1>..<filen>, as opposed to package mode (i.e. ajdoc <pkg1> <pkg2>..). It works in both modes now.