Go to :
Admin ---> Plugins ---> "WYSIWYG Editor"
and check the option :
"Allow other content to be uploaded, e.g. Flash, PDF"
and save changes.
On the editor you'll have now a new tab ("Upload") on the link dialog :
You said that you using the default editor and can't seem to find the pdf file upload tool.If you want to do that ,you can just try some free trail from pdf processing SDK.That would help you out.
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