I have no idea what you think "the plain Java API files" are.
The second link is not a git repo. It is a family of git repositories. Each row in that table is one git repo. The first link is for instructions on how to use Android-supplied tools to clone all of those repositories.
If you think "the plain Java API files" refer to the java.*
and javax.*
classes, they are from the libcore
repo.
If you think "the plain Java API files" refer to android.*
classes, they are from the frameworks/base
repo.
Other repos may be contribute other portions of "the plain Java API files", such as Apache HttpClient.
If all you are trying to do is poke through the code, I recommend Google Code Search. For example, I refer to the Android source code frequently, and I don't have it downloaded.
[Edit]
And if all you want to do is develop android applications, you don't need any of this; just download the SDK