First, you can build your application and copy the contents of the \bin\release folder (not obj) and if the user has the right version of the .Net framework installed, it should work.
However, you can also use CLickOnce, and host the deployment on a network share or web server, and then the user can install it and you can push incremental updates and have them install automatically.
If you are not using the Publish tab to create a deployment, then you are not using clickonce, regardless of any settings. What manifest are you referring to? You usually only get a manifest when you use Publish.
Next question, you say you are allowing the user to split a file into different files. Where are you putting them? I suspect this is your real problem, especially if your users are using Windows Vista. Vista only allows you to write to a couple of locations on the disk, and "C:\" is not one of them. You might want to programmatically create a folder under LocalApplicationData and stick the files there.
To get the path to LocalApplicationData:
string userFilePath = Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData);
string myDir = Path.Combine(userFilePath, "mycompany");
if (!Directory.Exists(myDir))
Directory.Create(myDir);
string myFile = Path.Combine(myDir, "this_is_my_file");
RobinDotNet
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