Can't get Visual Studio's "Publish Web Application" to work

I converted a small Web Project to a Web Application in Visual Studio 2010.

When I publish the application via FTP it will delete everything at the destination. And thats it...none of my files get uploaded.

Now, If I select "Replace matching files with local copies" it uploads all my files but it does run my Pre/Post Build commands but never uploads the resulting files (the Build Events create .min.js versions of my JS files).

I figure that whatever I'm doing...I'm doing it wrong.

Help me please.

UPDATE

So, the .min.js versions of my JS files weren't actually in the project. They were created successfully on each build...but they didn't show up in the Solution Explorer. So, I 开发者_StackOverflow中文版put them there and now it works okay.

Now my problem is that I don't want to see my Release build's .min.js files in Solution Explorer...ever. Do I just have to deal with it or is there something I am missing?

So, the answer was to "Add > Existing Item" to the project to include the minified versions of my scripts in the project.

As for the other question: "ow my problem is that I don't want to see my Release build's .min.js files in Solution Explorer...ever. Do I just have to deal with it or is there something I am missing?"

I'm going to go with "I just have to deal with it" as the answer.