The first option of adding an application with source files has done nothing but cause me problems. First off every time you 'update files' it copies the application from your local deployment folder to the server deployment point. This seems like a pretty big waste of time/bandwidth to me. Also, and a lot more annoyingly, is that since it is touching your files on the server, well that means that it is touching your files on the server. If you make a small change to something, or think that you're making a small change to something you might just be erasing your application install point on the server. This has a lot of implications that I just was not happy with. I lost several small packages that I made and it took me a little while to figure out what was happening.
The second option of adding an application that is elsewhere on the network is just what the Dr. ordered for me. I don't know why the first option is there, but in the future I will not be using that. Maybe for someone there is a valid reason to use that option, but I would rather physically touch the files on the server myself rather than have the tool update stuff for me. When using this option I suggest not even using the applications folder that is part of the network deployment point. I have my own network share for applications and I copy the files over myself and I just point the new applications wizard to it.
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