How can app file be treated as a file in Package Explorer for Mac OS X?
You can't talk Eclipse into treating app bundles as files.

Mac apps are actually "bundles", which are special folders, not files. The Finder treats them as files, but anything that uses lower-level file system APIs will see a .app file as the folder it actually is. 

If you look at the appify script on Github, you can see that just making a few plain folders in a specific structure will cause the Finder to treat them as a file.