Guys, the original question is really simple -- it isn't actually a problem at all. In Eclipse there are two ways of displaying the packages. There is a little down arrow in the top of the package pane that brings up a menu and in that there is Package Presentation. There are two options "Flat" and "Hierarchical". If you choose flat it will show the full package names "com.ejer.first" and if you choose hierarchical it will only show the full name if there are no other sibling packages. For example, in hierarchical if you start by creating a package called "com.ejer.first" then it will show it that way, but as soon as you create another package called "com.examplemod" it will then show them both in a directory tree "com > ejer.first" and "com > examplemod".
In other words, your package is still properly com.ejer.first, it just displays as a folder explorer.
So basically there was nothing wrong in the first post. That is the way hierarchical view looks.