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Application / Package confusion

Hello all,

when I build my application, I

1) start with a jar-file,
2) then use JarBundler to turn it into a proper MAC application and
3) then use PackageMaker to turn the MAC application from step 2) into an
installation package

All of this is working fine, so now I am trying to understand what actually
happens (the motivation being that I want to use ANT to automate the build
on a windows machine), and I'm getting very confused:

I understand that the application is nothing more than a directory with the
suffix ".app" in its name, a specific folder structure and some specific
files like "info.plist" etc. Right?
I also understand that the package is nothing more than a directoy with the
suffix ".pkg", a specific folder structure and some specific files. Right?

What I do not understand is where my application ends up inside the package
file. When I open the package, I see a file called "archive.pax" which I can
open with any decompression software (I use WinRar), and this "archive.pax"
file seems to be identical to the jar-file that I started out with.
My question then is: what has happened to the application I created with
JarBundler? Is my step 2 necessary at all or could I also directly create a
package from my jar file? I hope this won't confuse you as much as me...

-Thomas
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