How do I distinguish between a package file and a pdf file with an attachment?

Q: How do I distinguish between a package file and a pdf file with an
attachment. For now both are considered to be the same and there is no
distinguishing property to identify separately
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A: To check if a given PDF contains a collection (i.e. is a package)
you could use the following line:

Obj col = doc.GetRoot().FindObj("Collection");
if (col != null) { ...
}

To work with packages you could use the code along the lines of
PDFPackage sample project (second code example):
  http://www.pdftron.com/pdfnet/samplecode.html#PDFPackage