If with files you mean in what class the
BinaryData folder is used, then you can find references of it in the following locations (in DXA 1.1 .NET):
Sdl.Web.Common\Configuration\SiteConfiguration.cs line 31
Sdl.Web.Mvc\Statics\StaticContentModule.cs line 58
If you then take a look at
Sdl.Web.Tridion\Statics\BinaryFileManager.cs you will find the
GetFilePathFromUrl(string, Localization) method uses it, which in turn is used in:
Sdl.Web.Tridion\Statics\BinaryFileManager.cs line 91
Sdl.Web.Tridion\Statics\BinaryFileManager.cs line 184
Not sure if this all is helpful, since your question does not tell me whay you are looking for this. Maybe you should consider editing your question and letting us know what your problem is, so we can provide a more detailed answer.
The DXA 1.1 release (the zip you mention I assume) currently only supports .NET, there is no released Java version available yet. We do have a pre release in Java, but that is not for the faint hearted. You have to build it yourself and there is little to no documentation to guide you. We expect to release a DXA Java version (documented and tested, equal to our .NET release) in October 2014.
Reading your updated question again, I think you have a wrong expectation of how SDL Tridion and DXA works. SDL Tridion transport packages are zip files, but these do not contain a web application, they could contain pages of a web site (if you use a static publishing model).
DXA is an MVC web application, where we publish content from the CMS to a Content Data Store. The MVC web application will assemble the views upon request and fetch the published content from the Content Data Store, which means your web application must be already installed, you can't publish that itself from SDL Tridion.
Maybe it helps if you read the DXA documentation, but keep in mind my first update, it currently only supports ASP.NET MVC.
If you are looking for the source code of DXA, you can find that on GitHub as is also explained on our community site https://github.com/sdl/dxa-web-application-dotnet
If you want to build it in Java, as mentioned we have its unfinished source code also available on GitHub (in the develop branch) https://github.com/sdl/dxa-web-application-java/tree/develop