Okay, here's what happens.
I have an add on package that I wanted to package up with a main program. The problem is the add-on doesn't have a .exe file so I had to make a .bat file to open it which, unfortunately, is not recognized as a user entry point. So I converted the .bat file into an .exe file so that I could create a user entry point to that file.
This is a similar situation to opening a word document and it automatically opens Microsoft word. Only in my case I would create a batch file to that word document then convert it to an .exe file so I could create a user entry point for that document.
So in my case after it's all packaged up and I run the user entry point I get an error, could not open file. Is this what I would call a linked file? I'm packaging it up under isolation write/copy mode and not in merged mode.
Any ideas?